It's difficult to answer without seeing it. Yes cistern is held to pan by 2 wingnuts. The neatest and easiest way is to take the pan and cistern out, tile the wall and floor and put it back in again.
Most times the waste on the pan is on a connector that would allow you to have the cistern 15 mm away from the wall and not alter things too much, the cold feed into the cistern should alllow a tiny bit of give if it comes out the floor, failing that use a flexible hose to connect to the cistern and then you will have enough give/play.
With a 7mm wall tile and a 4mm bed of adhesive you are only talking 11mm, the thickness of a pencil? That will not transpire to much altering of pipe angles at all.
Try slackening the screws that hold the cistern to the wall and moving it, you may be worrying about nothing.
As far as screwing the pan to the floor - good silicone will stick sh*t to a blanket, if the cistern is screwed up tight and the pan is siliconed to the floor it won't move.