1) Do they count as terrain for all purposes? I cast Commune with Nature last night and it seemed odd to have it effect a stronghold. <shrug>

2) Unless explicitly stated, Landmarks are allowed as long as both players agree beforehand?

1) Not sure about this one but I would say yes. The rulebook (p.65) states: ''Unless explicitly specified otherwise on a Landmark's Summary card, the following terrain rules apply to all landmarks...'' which means that Landmarks are treated as terrain, so the movement restrictions can be ignored for the Landmarks as well.

2) Correct. It is simply a matter of determining beforehand if Lore Master Landmark rules are in effect or not. (Rulebook P.65 as well)