Oh dear I think I see what's going on.
Page 5 of Rulebook wrote:
> Conquering a Monster occupied Region
Whenever a player successfully conquers a Region occupied
by Monster tokens, he immediately draws a marker from the
top of the stack of Popular Places & Righteous Relics, and places
it into the Region just captured.
The player may also receive some additional markers or
tokens depending on the special powers or benefits granted
by that Place or Relic (see Righteous Relics & Popular Places
on p. 13-15).
I believe OP has misinterpreted the rules to mean that you have a Pile of Popular Places and a pile of Righteous Relics and when you conquer a monster occupied region you draw a tile from both piles ie "draws a marker from the top of the stack of Popular Places & Righteous Relics". At least this is the only way I can see to misinterpret the drawing RR/PP rules.
However there is just supposed to be 1 giant pile of Popular Places & Righteous Relics mixed together and when you conquer occupied region you draw 1 tile from that giant pile.
So in essence OP's "variant" is actually just the real rules and OP has actually been playing with a variant the whole time.