I know the answer, but it's been 7 years since I shop for an alarm and I'm not sure if things changed. So here are the questions:

1. I can still use and keep my factory keyless remote to operate just about any basic brand alarm such as DEI/Viper. True/False?

They want to charge me $50 to do this.

2. Is there special wiring involve that would make it more complex? Better/Worst from an electronic point of view.

I like the factory remote because I have remote trunk release, etc. But I just like the factory unit better than the traditional two buttom remote that comes with the alarm. I don't want to press some combo buttons to open the trunk, etc.

 

Well #1: FALSE
I might be wrong but from what I currently know, you cannot integrate your your factory alarm remote with the aftermarket alarm brain. At least as far as Honda/Acura is concerned.
If you really like the functions on your factory remote they can all be duplicated on the aftermarket DEI remote...I.E... ARM (lock), Disarm (unlock), AUX=Trunk release.