Since Secret Shops have max total spawn per run, don't spawn 2 in the first 3 stages. You might have enough gold for the first shop, but then you'll have nothing for the 2nd just one room / stage later.
Maybe have a buffer like max 1 spawn in first 5 stages, max 2 in first 10, etc
Something like that.
Because it's not really random .e.g it's 100% impossible to get a secret shop to spawn 15 times in a run. There seems to be a count keeping it within a certain range over time within a run.