Would this USB detection circuit work as expected?
Your original system was uncertain as the data sheet does not provide enough information. I'd guesstimate that it would probably work but this is not ceryain.

Your second method, with FTDI Vcc and VccIO both being operated from +5V has more chance of success. A possible issue is that the =%V line will now be one Schottky diode drop below Vbus but U4 is connected directly to D+ and D-. I do not know what level D+ and D- reach when at their maximum positive value but if they reach VBUS then the IC has SLIGHT voltage above Vcc applied to pins 15 &amp; 16. I would expect that this would probably not cause problems as the IC is intended to operate "robustly" in an interface environment where "such things happen" but it may be worth keeping in mind if strange things happen subsequently. This may be covered in the data sheet - an exercise for the student :-).

Stop Press: I just checked data sheet - the two USB data interface lines are nominal 3.3V level signals so the above is a non issue. I'll leave it here as it covers something which can occur in this sort of situation so is instructional.