For example, I have just bought a laptop one of my daughters to take to university.
It came with Symantec anti-virus software (three month trial), which I detest. The VERY first thing I did was remove it and put my own preferred solution on. In fact, the machine has now been "personalised" to such a degree, it's hardly recognisable as the original product. And by the way, it's considerably faster than the manufacturers configuration. Why? Because I've got rid of all the rubbish they had auto-starting on boot-up.
Looking at this logically, you buy a computer to use. Does that mean in order to maintain a warranty, you are not allowed to use any of your own software for a year? I don't think so!
The other side of the coin is, I wouldn't expect them to sort out a software related problem; most don't anyway. The best you could hope for is a reset to the original configuration, and frankly, that is not unreasonable. You cannot expect any manufacturer to put your machine back to your OWN configuration, it's just not feasible.
I would expect however, in the event of a hardware failure, for it to be fixed under warranty, as in general terms, there is no way software can play a part in hardware failure.