I play the game on Kongregate, but I found out that the game has slightly different versions in other sites. The most important difference is the in-game timer for each individual level. In Kongregate, for example, the timer start right when the level is loaded and ends when picking the puzzle piece. In NotDoppler for example, the timer is reset on every death. Thus making the in-game timer unreliable in case of a checkpoint-death in a level.
Also, there may be differences in the levels layouts themselves (Kongregate and NotDoppler also differ by the layout of level 3)
So, to make it easier, all runs of the game must be ran exclusively on Kongregate, to make a fair competition between all runners.
Kongregate - https://www.kongregate.com/games/TawStudio/mr-bree-returning-home
EDIT: Recently I found a very useful program for playing many of the flash games out there. It downloads the SWF files locally, and play the game locally on the computer (even offline), but it makes them think they are being played on the browser. "Mr. Bree Returning Home" is there too, and I checked that version, it's identical in gameplay to the Kongregate version (although some of the logos are different). Playing the game on this version is allowed, if you want. https://bluemaxima.org/flashpoint/
Level 3 changes depending on which site so maybe that should only be played on kongregate (or maybe you can add a filter for which site you play on? I don't know)
I don't think anything else changes in the rest of the run so only level 3 and full runs should be done on kongregate exclusively imo, as long as you dont die in the other ILs (they're identical otherwise)