Does the FTDI have a solder jumper to cut or install to select 3.3V or 5V out?
It does matter if you have other devices connected to Vcc as well. If they are strictly 3.3V, you will blow them up. With that in mind, it would have been wise to route the Vcc pin through the regulator as well. Ultra low drop regulators would only take away maybe 0.1V or less at small loads.