I won't argue this any further. I will say that the reason to put the car back to original condition is not to conceal anything or defraud or take advantage of the dealership. The reason you put the vehicle back together and remove the remote start is because if you leave it as it is, with wires cut, splicing done and a number of aftermarket items installed under the dash and maybe the hood too, the first thing that will happen is either the repair tech or the service advisor or the service manager or possibly all 3 will take one look at what has been done and automatically say there is no way they can warranty any of the repairs, it's all CP -customer pay- because the installer did the damage. In fact they would charge more to put the car back to original condition. If the car is as close to stock condition as possible and doesn't have evidence of incorrect installation and wires and alarm modules going all over the place, there is a greater chance the service manager will be willing to work with the OP to get the car fixed. Sure, the OP may have to pay part of the repairs, because it's their own fault the car won't start. It's up to the OP to own up to what they did if they expect the dealer to assist and 2. It's up to the service manager to decide whether to warranty any of the parts and/or repairs.
The only other reason I said anything about removing the remote start is because I have dealt with dealerships before for this exact same situation. They take one look at all the "stuff" under the dash and immediately refuse any help at all. But if the vehicle comes in clean, there is a much better chance of the dealer being willing to assist. It is more due to the fact that a dealer service tech has absolutely no idea how to wire a remote start or alarm, much less how to troubleshoot one. The OP's car would not start after they attempted installation of a remote start unit, so it is a very good idea to remove the remote start so the technician can fix the car and get the car starting again. Then the OP can have the remote start installed correctly if he chooses. In this case the OP is pretty sure he knows what is wrong and will fix it himself so this argument is pointless.
This situation does kind of remind me of the many posts down in the sales and promotions section of guys using coupons and rebates working the advantage and going to multiple stores with the same coupon or using multiple names and addresses for mail in rebates and trying all the tricks to save money for oil, filters, parts, and God only knows what else. If what I suggested to the OP sounded dishonest to some of you, I suggest you look in the sales and promotions forum so you can point out even more dishonest practices.
I am done with this post.