Over the years I think the meaning of the term may have changed slightly, but I think it was always related to scientific stroke making or precise stroke making (the use of that term predates scientific course-making). A scientifically designed course requires precise stroke making - good shots are rewarded and poor shots are punished. There is also an element intelligent thought that is required. Golf architecture was being looked upon or studied for the first time, where proper design ideas and elements are promoted and archaic ideas are discarded...that is where the idea of fairness come in. For example the cop bunker placed at formulaic intervals from the tee is not an example of a scientifically bunkered golf course - it does not challenge the expert while overly punishing the average golfer. Also blind shots are something to be avoided on a scientifically designed golf course; OB is another unscientific element.
By the late teens and twenties modern American golf architecture (the American Movement) really promoted the idea of scientifically bunkered or laid out golf courses, this in contract to the British model, which was less penal leaning. The epitome of American scientific architecture were heavily bunkered courses like Pine Valley, Oakmont, Inwood, Lido and Hollywood. And as Americans began to dominate competition a theory developed that the American scientifically designed golf course produced a superior golfer. This domination eventually resulted in pressure within Britain to adopt a similar American architectural model in order to compete. Here are some examples of the terms use over the years, and clearly saying it was synonymous with modern is a gross over-simplification.
Henry Leach (1911): "Now during the last two or three years there has been given an enormous stimulus to the study of links' architecture in this country. It has been made the most exact science, and is studied as such. There are, as one might say, professors and students. All the old theories and practices have been overhauled, and in most cases condemned. New courses are being made on entirely new principles of length and bunkering. It no longer does to put a short hole in just where it seems convenient, as they did in the old days at St. Andrews and Prestwick. It must come at the right place, and be bunkered according to the right theories. And so forth. Whether the new courses that are being made, and to the points of which all these new theories and results of study are being applied, are any better or more interesting to play upon is a question which we need not discuss. It is after all largely a matter of temperament. Certain it is that some of these new courses are really very perfect from the scientific point of view. Good shots get their reward, bad ones are punished, and the golfer is tested at every point of the game and made to learn all the different ways of doing the same thing."
H. Mallaby-Deeley (1914): “No course, however difficult, can be a good one if it is unfair and I notice that the latest tendency is to make things difficult by making them unreasonable in respect to hazards and the position of the hole to the green. This may produce high scoring, which seems to be the object of many golf architects, but it is not scientific course construction.”
Max Behr (1915): "Very different is the first short hole at Princes', the new and scientific course next to Sandwich. There the green is heavily bunkered in front and on the sides and is not more than thirty feet wide at any point although it is at least sixty feet long. Also the green is plainly visible from the tee, which is the most essential feature of the mashie pitch hole. It is plain that if the player succeeds in placing his ball anywhere on the level part of such a green he has a good chance of getting his two. He does in fact play for a two. And if he makes the stroke correctly he ought to have a perfectly sure three; but if he makes an indifferent stroke which still leaves him on the green more than six or seven yards from the hole he ought to have a very difficult long putt, and a good chance therefore of taking a four."
Arthur Croome used the term here in 1925 to explain why the casual visitor (especially if he be an American) would not appreciate the subtleties of the quirky Dowie at Hoylake, "especially if he be on American accustomed to scientifically constructed courses of his native country."
Walter Travis (1920): "Moreover, the fairways are then not of that adamantine character met with in July, August and September, when the ball "runs a mile" and spoils the legitimate playing qualities of the holes, converting three-shotters into two-shotters and ordinarily long two-shotters into a drive and a mashie, and so on, to say nothing of almost completely setting at naught the proper values of hazards, no matter how scientifically arranged."
Glenna Collett (1925): "On the whole, I consider the American courses more difficult, although they offer very different playing conditions. Being for the most part by the sea the British links are flatter and very rugged and have more natural hazards. The fairways are narrower, and the ground is very rolling—especially at Sandwich, where it is almost bumpy, and your ball is apt to glance off in any direction. But in layout our courses seem more scientifically designed to prevent low scoring. There are longer and more difficult par four holes. All my scores while I was there were better than what I can do at home."
Here is a quote from 1925 regarding Oakmont: "From every tee. and for every second shot the player looks out upon a disfigured surface, upon up-thrown earth works, exposed deposits of grey sand, and other yawning chasms which invite disaster to the timid, but in between these artificial hazards, carved in irregular formations are acres of absolutely perfectly groomed fairways upon which no poor or indifferent lie is ever found. Herein lies one of the greatest charms on this scientifically built, and very exacting course."
AW Tillinghast (1927): “What a contrast our up-to-date American courses afford! Our golf architects etch pits right into the fringe of the green. They are set close in on either side to catch a slight error. The greens are scientifically contoured to hold a bold approach. Such tightly bunkered greens make for meticulous accuracy in approaching. Slipshod, hit or miss methods won’t serve. A fraction of a foot off line may mean the difference between a ball on the green and a lie in the bunker. Under the circumstance, American players have just got to develop perfect direction. Our intelligently bunkered courses are a stern, uncompromising school, but they graduate golfers able to weather the stiffest examination.”