For the All Secrets category do I have to just get all 5 secrets and stop time once I get the 5th secret or do I have to get all 5 secrets and beat the game as well and stop time at the same time as in any% or glitchless? Was not too sure since there is no category rule set for the category.

Nope, you just have to collect all 5 secrets. You are allowed to exit and enter different levels, but for lag purpose I'm removing the time that you aren't in-game (the timer is "paused" while you are in the levels menu.) Thanks for asking, I'll clarify the rules for this category.