The ideal is to aim for 90*, brakes applied. Disc brakes self adjust, so that makes it easy. If using drum brakes, the self adjusters should be used & that will maintain a uniform pedal position.
A few degrees either side of 90* is ok, but aim for 90*. It will NOT wear out the seals because [a] the seals are fitted to the pistons which are a tight fit in the bore, & the pistons do the locating, not the seals the seals are made of soft COMPLIANT rubber to conform to shape changes.