Arduino Uno-style Reset Circuit
I recall having exactly the same issue on a recent design with the FT231X. I'll have to check tomorrow on our original issue and solution but I reckon the answer is to reprogram the ftdi chip to invert the DTR function (maybe, or maybe you need to use a different pin) and use it to drive an open drain FET on the reset net. 

EDIT:
Sorry, I have completley mis-remembered our issue. It was with using CBUS3 as a power enable on a FT230X (not full handshaking version). Still, if you can invert your signal the suggestion should work.

I have to say I'm a little confused though, the DTR functionality is for RS232 handshaking and I can't see on the datasheet how you can use this for reset?