The percentages aren't the same but the proportions are still the same.
Consider three categories: Hot Spots, Warm Spots, Cool Spots.
Hot: Independence Square, The Witch House, Unvisited Isle, Woods
Warm: Black Cave, Graveyard, The Unnamable
Cool: Hibb's Roadhouse, Historical Society, Science Building, Silver Twilight Lodge
Arkham has 10 Hot each (15.2%), 6 Warm each (9.1%), and 2 Cool each (3.0%).
CotDP adds 2 Hot each (11.1%), 1 Warm each (5.6%), and 1 Cool each (5.6%) plus 3 "Other/" Mythos (16.6%).
DH adds 2 Hot each (5.6%), 1 Warm each (2.8%), and 0 Cool each (0.0%) plus 25 "Dunwich" Mythos (69.4%).
KiY adds 3 Hot each (11.1%), 2 Warm each (7.4%), and 0 Cool each (0.0%) plus 9 "Other/" Mythos (33.3%).
KH adds 2 Hot each (9.1%), 2 Warm each (9.1%), and 1 Cool each (4.5%) plus 4 "Other/" Mythos (18.2%).
BGotW adds 2 Hot each (8.7%), 2 Warm each (8.7%), and 1 Cool each (4.3%) plus 5 "Other/" Mythos (21.7%).
TOTAL now has 21 Hot each (9.2%), 14 Warm each (6.1%), and 5 Cool each (2.2%) plus 21 "Other/" Mythos (9.2%) and 25 "Dunwich" Mythos (11.0%).
So depending how you mix and match, the percentage of what you have will change. However, every "hot" gate will have the exact same number as every other hot gate no matter how you mix the expansions. I am not sure how Innsmouth will act but I assume it will follow the same pattern.
And while this wasn't mentioned above, Dunwich makes Wizard's Hill Hot, Gardener's Place Warm, and Cold Spring Glen, Devil's Hopyard, Whateley Farm all Cool. Mixing JUST AH and DH, will also make these places consistent with their AH counterpart. For example, all Hot will have 12 cards each, all Warm have 7, and all Cool have 2.
One other note: A gate opening is always paired with the same Clue location (and Gate Bursts are always paired with the same 2 Clue locations). However, due to Rumors, the Clue distribution is not the same as the gate distribution. So when a location is Hot for gates, its corresponding Clue location is Hot for Clues in general but it may not be as hot as onther Hot Clue location.