Honestly, every PC I've ever bought had the sticker that warned about voiding warranty if the seal was broken, except perhaps with my first Atari 800XL. I know my A3000 did, because I recall throwing a Supra 2400zi modem in it myself and then later taking it in with bad memory in it and there was no issues with warranty.
I always saw it as an ass saving measure on the part of the manufacturers, really. Some clown comes in with a CPU ripped off the board, you can wag your finger at him and say "sorry, you did this yourself when you should have taken it to an authorized service dealer", but in my experiences they never gave 2 craps about some guy just putting a modem in a machine if a completely unrelated problem later popped up.
In regards to the X1000, from day one I always felt the biggest mistake was the fact they didn't simply offer an Acube style mobo only option for system builders. While the X1000 may be attractive to some, there's a huge number of people that find prebuilt machines absolutely reprehensible, whether they be an Amiga or a windows pc. I don't need a prebuilt machine, I refuse to pay the price of them when I am entirely capable of building what I consider a much more attractive system to MY specs for less cost. Last prebuilt PC I bought was well over 10 years ago, and I wouldn't have bought my SAM if it was only offered in prebuilt form.