I've tested it, and it keeps some perks, but the Experimenter perks are lost.
I would advise to reset the perks somehow. The console command "removeperk" can work but it does not refund perk points, which would require "addperk" after that. Legendary might be an option if you have enough ingredients to get to 100 again, but I would say the best option would be spending a dragon soul to refund your perks with the black book of the Dragonborn DLC.
Also, reset the perks before installing the mod. If you use the console commands option, that will probably not be a problem since you can just fix everything.

Looks good! What do you suppose wold happen if this was used on an existing game with the skill tree part filled? Thx