I just give fact: on my frame, with a 42.5 or may be 43.5 or 41.5 if my measurement is not correct, the brace between the seat stays hit the seat tube (you misunderstood my post, I never talked about tire, but possible things between the brace and the seat tube, like mud).
It depends on the shock/frame/pressure/riding style if there is a risk or not. If not, fine, may be the suspension kinematics is progressive enough that it is not possible to bottom out.
FYI, I will use a non trunnion shock with 38 stroke, because I have it, and I do not like this trunnion mount style (am I the only one thinking that an aluminum bolt should play the role of the axle?).
Read this topic...please.... There are several people (incl me) riding the bike in size medium and large with a 42.5 shock without any problems.
And mudproblems? It's not a tyre clearence problem.
But I dont think there will be much difference between 100mm travel and 105/110mm...so pick a shock pricewise.