DNGoldie:
It's a good question you ask--one that's come up on here before.
It's true that square tees (or squared off tee tops as you describe them) don't blend in well with the overall curving and natural lines of sites or even the architecture that might otherwise blend into those natural lines or attempt to.
One would certainly wonder why that would be when most architects might attempt to blend the remainder of their architecture with natural lines.
To even begin to answer that question tees should probably be looked at closely as to their evolution in golf as well as how they were perceived by architects who were the most sensitive to blending everything possible to the natural lines of sites.
Even those "Golden Age" architect's who dreamed that someday modern technology would allow architects to almost completely hide their hand from what was natural admited and conceded that in the case of greens, fairways and tees that might never be completely possible, The obvious reasons are those three things were simply the primary necessities of golf that just never could be compeletly natural looking or seem completely natural in a otherwise natural setting!
Ironically those particular "nature inspired" architects added a fourth golf architectural feature to that list of greens, fairways and tees that although they conceded was not particularly fundamental to golf had become an apparently fundamental feature--bunkering!
Why bunkering became almost fundamental to golf and remained part of golf architecture in areas where bunkering was clearly not natural is a very interesting evoltution itself that probably indicates the original allure and primacy of the original linksland and the original linksland courses where natural bunkering was central to the game!
Architects have tried their best in many cases to design greens, fairway and bunkering that somehow blends with the natural lines of any site but tees seem to have escaped that tendency to try to "blend" with nature for some reason.
Why that is has to be difficult to answer conclusively if at all. It may be that golfers have insisted on a very defined and identifiable starting point that may line them up at their target in a general sense. Apparently tee blocks on otherwise unaligned tees do not do a good enough job of that!
And then it's quite interesting to note that the separated tee feature is quite a late entry into the evolution of golf and also architecture. There was a time even following the orginal rules of the game that a rule of procedure was to tee off within one and then two club lengths of the preceding hole!! Think about that!! That's amazing to consider today and would seem almost ridiculous! How easy would it be to sink a six foot putt with those conditions and rules?? That simply indicates how rough the playing conditions of golf once were!
But every single kind and type and look of tee has been tried architecturally. Some were unbelievably shocking looking during the crude "geometric" era that looked something like funeral pyres with periscopes and such! RTJ created the super long but very defined "landing strip" tees and others like Muirhead tried every shape and form of "freeform" tees, possibly to try to blend them with the lines of nature or possibly for other reasons such as a variety of golf angles to play.
It seems even in otherwise "natural looking" architecture today the square tee box is making a return! But square in what architectural sense is probably a better question for you to ask and have answered. In many cases the actual architectural construction builds up the tee box to be very identifiable and also square. In other cases the constructed architecture is not so identifiably square but the mowing patterns are.
As to why tees may need to be built up (or even square) for reasons of construction and drainage and such others on here could answer that far better than I could.
But there is a new tee look coming out now that might be a return to some of the styles of the past. That's one that blends or melds the tees into natural grades as to be almost unidentifiable (at least archtitecturally). Some like GCGC's tees are built right on grade. There are some others like #7 Friar's Head and possibly #14 Applebrook that are almost completely unidentifiable architecturally and also in mowing patterns. In fact these ones blend completely into the overall surrounds and all that can be identified as tees are the tee markers themselves.