You raise an excelent point about the laptop, and how the mobile industry seems to think locking down phones is OK, but we would never stand for it on our PC's. I guess it comes down to the mentality of it. The mobile industry has grown so much, so fast that the carriers/manufacturers could not possibly hope to deal with all the "warranty" issues that people would cause if their boot-loaders were unlocked. Nevermind the inherent problem unlocked boot loaders create for the carriers in terms of being able to swap out radios and such. It's unfortunate, but it's the industry and we've all, basically, agreed to let it be that way by purchasing these devices under these terms.
As for "tracing your ROM" you are partially correct. While they could, most likely, find a reference to the custom ROM online and get a list of the changes, they won't be able to actually look at the code itself that is contained within that ROM. And even if they could, the amount of time that would be taken for someone at HTC to go through all the code for a given ROM and make a determination of whether or not the problem you're having is caused by that code would be immense, to say the least (and I say this as a software developer myself). They simply don't have the resources to realistically expect them to try and disassemble, analyse and debug a custom ROM to determine whether or not a given problem is caused by the software or not. This is the *reason* that they make you agree to the terms of voiding your warranty when you unlock the boot loader.
I'm sorry if I sound harsh, but it is what it is. And, frankly, you agreed to it. HTC is really not at fault here. They have to protect their profit margins, and that seems hard enough for them right now. I'd say that if you don't like it, you can spend your money with another carrier/manufacturer, but the truth is that this policy is pretty much industry standard. Sorry