depends on the mods. dealers might deny you warranty related to a certain part. for instance if you have a chip they might not warranty your engine, but your brakes are obviously still under warranty.
*some* (more like all) dishonest dealers try to pull shit on you to make you pay like denying your transmission warranty because you have after market wheels and shit like that (seen it happen)
usually all mods or most at least are reversible. i try to avoid certain mods like would put a SC or TT on the engine for instance, im not a fan of aftermarket exhaust, but i'd do all cosmetic stuff.
will they perform service? again depends on what the mod is. for instance if u drop your car on springs they might not warranty your shocks/springs any more.
what kind of mods are you thinking?