The keyless fob and factory alarm still work with the remote start (it arms and disarms when you lock/ unlock). I haven't checked whether the factory remote will unlock the car or not when it's running (on my 2001, the keyless entry system was disabled while the engine is running) but I always use my Viper remote.
From my experience the factory lock and unlock buttons on the fob won't work when the car is running via the remote start, you will need to use the viper remote for that. Not sure about the smart key, but I would imagine it not working either...I remember on my old IS if the car is running the smart key lock and unlock function do not work (ie. if you try to press the button on the door handle and/or pull the handle to unlock)
Regarding the push-button start, systems now can handle that option. Even pit stop mode still works I hear (cold day, running into the bank or something, leave the truck running and take your key with you and lock it).
pit stop mode should work with the smart key, but I guess with the smart key you would need to remember to take the extra step of shutting off the smart key by pressing it before leaving even though the car would still be running due to the pit stop mode (similar to people with regular keys and turning it to the off position and taking the key with them
), or else it'll run indefinitely.
I thought all the remote starter and bypass module do is trick the truck into thinking the key is in the ignition. What requires it to tie into the ECU?
There's two ways that the aftermarket bypasses operate, one splices in between the IMO/IMI signal wire and it basically intercepts the signal coming from the key transponder and replicates it to the immobilizer ecu. The other way piggybacks onto the TXCT and CODE wires at the transponder receiver and captures the key code from the transponder, which is later used to send to the immobilizer ECU. Keep in mind most bypasses also need to be connected to the CANBUS signal in order to operate.