I understand the appeal of crossovers to architects.....it is a quirk feature that is rarely duplicated elsewhere and can help to make your course stand out. I sought out potential crossovers, and finally found the perfect opportunity at Superior National in Minnesota.
The par 3 second plays over rushing rapids (imagine a course with views of Lake Superior, and those aren't even the prettiest holes). The third involved a cart ride back over the river, but there was room to put the back two tees next to no. 2 green, and have those players tee off over the river. Since the cross over is water, there is no chance of players being in danger.
Von Hagge did that at a course in DFW, with parallel par 3 holes over a pond, but he switched the greens so the cross over is over a pond, again eliminating the safety issue.
In this day and age, I consider the pace of play issues that these create of equal importance on any reasonably well played course. Oddly, I had this discussion just yesterday, just talking about combined tees, which also look kind of neat. However, when you realized one group or the other has to wait to play, you quickly have the follow up realization that a bit of separation works better for the course, and if form follows function, crossing holes and combined tees or greens really aren't so "cool looking features" as to warrant inclusion. Again, on low play private clubs, I think you would have more latitude, but really, just because some old courses have them, and we are searching for "cool features" these wouldn't be top of mind for most architects, for good reason.