As Raymond said, if the watch is significantly modified, Patek is warning that they may not accept to deal with the consequences. And I think that's normal.
Of course, if you change your bracelet to strap and go back to bracelet for a servicing, as long as they have a normal 5960/1A in their hands for the service, there is no problem.
The thing is that in the real, people may change the bracelet, make a scratch or hairlines, damage the lugs' holes, attach the strap the wrong way and make the watch fall etc... For instance it is suggested that you avoid combining two different materials in case of frictions (like a strap steel pump in a gold lug's hole as it will widen the hole).
I can understand that a brand doesn't want to deal with this sort of issues. PP does this to prevent any wrong use of the watch as some owners can do what people here would not.
That's just a kind of safe warning in order people pay attention to what they do.
I imagine it may be the same for Rolex if someone changes the dial of a watch.
Otherwise, if the owner does things well, they won't see it and the warranty will be still valid IMHO.
Best, Mark