I love my Autocover (see my many posts raving about it). I would never own a pool without one.
I added an SWCG this year. So far, no adverse effects. I will note too, that my salt level was already 1800ppm when I "converted".
The one thing I did do, that the installers didn't, was to try to bond the various pieces of the autocover system (since mine is deck-mounted). I connected the tracks and brackets together with bonding wire and then ran that back to my equipment bond spider. No idea if this was necessary.
Aside from all the usual awesome benefits of an Autocover (like safety and keeping most debris out of the pool), I think it also keeps my pH from rising as we generally only open it for a couple hours a day. Lots of people have pH rise, but mine seems quite happy to sit at 7.5-7.6 for weeks without adding acid.