Nifty! So, I know a few more things now (it gets easier to tell what's going on when you've gutted so much of the stock wiring harnesses...). Probably the reason you don't have Nav/Radio in that scenario is that certain parts of the car (notably Nav/Radio, but I believe also things in the doors that normally don't operate when locked/off, like windows/mirrors) are powered *through* the BCM. The work you've done up there under the hood is bypassing the power control of the IPDM-ER, but not the BCM. The connector with the 3 fat wires on the BCM is where its power control function is at. The top left wire is battery input, and the other two are +12V outputs that buss to a bunch of interior things (one is "battery", one is "when ignition on", basically). I bet you'd get everything working if you also switch-bypassed across that stuff.
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