Ok, so I got a response from Gary. I'll place it at the bottom of this post.

My thoughts on his response, it sounds like he had the same problem you are having (ie: when you unlock the doors it also pop's the trunk) His solution was to wire the safety interlock to the solenoid like you should, then you can't pop the trunk while in drive. You would have to be in park for it to fire. Maybe if we can find the wire that ties the door console into both doors we could rewire it at that location. (ie: instead of splicing the wires out at the actual relay find the controller box, if there is one, hook both doors to the first click, hook the solenoid to the second click and hook the door console to the first click) That way, the console would fire just like a first click on the fob instead of like a second click on the fob.

I'm in the same boat as you, I can pretty much rewire things. But, I'm really a wiring newb when it comes to cars. So, I guess I better stock up on fuses before I start messing around
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Gary's Response 1
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It's not real simple, but I'll be glad to detail it to you when I get a few
minutes. And, just so you know, if you buy the garage door opener module
from Isuzu for $100, it could be wired easily to control a popper from the
"option" button on the factory remote. I wanted to do that, everyone I
talked to said "no way" including Isuzu factory people, so I did it my way
(2nd press of main button). After I did it my way, then I ordered the garage
door opener when I had a spare $100, just to check it out, and found out it
works on a 120V house current to 12v DC transformer. And all it does is
complete a two wire circuit. So, if I had it to do over (and didn't care
about the garage door opener aspect-which is pretty neat if you have a
dedicated garage for the Isuzu like I do- would be to wire the module as a
ground control on the primary side of a relay, with the secondary side
controlling the high amp current directly to the door opener solenoid. And
power the module with 12V from the vehicle, and throw the transformer away.
Thanks,
Gary Bucklew

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Gary's Response 2
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The thread you linked me to provides virtually all the details, although
it's pieced together from several posts. Do you have a specific question?
It's true, the down side of my method is that if in neutral or park, if
someone hits the "unlock" switch on the door panels (either one), the hatch
will pop. But 1) if both doors unlock off first press, and they do and 2) if
you wire the safety interlock to the shifter (as you should), there is
really no problem. I did this two years ago, and have only accidentally
unlocked the hatch a couple times, both while dead stopped. And I think it's
convienent to have a switch to pop the hatch in both doors-I use it all the
time loading and unloading my greyhound from the hatch.
Just some info.
Thanks,
Gary Bucklew