Well he did changed the skill codes in one way or another to make the skills unique, but he didn't change the skill GUID. It's up to him to fix that.
Or maybe you can include this Mod as an alternative
Mastery Mod (v.2) 
But I also feel that Mod also did not change the skill GUID, it's up to you if you want to include it or not.
@Viz if someone wanted to make new classes then what GUID's should that modder choose to avoid conflict with FEP+ and Variant?
Thanks for your time.
Well afaik.. the GUID is an identifier that is generated automatically every time you create a .DAT file by using GUTS. Every GUID is supposed to be unique and different from each other.
The only reason conflict would happen is when you copied the .DAT file from the original source and uses it directly for your mod without changing the GUID.
So to get a new GUID, use GUID Dumper in GUTS> Utilities. There is also a tool to generate the GUID without using GUTS somewhere in Runic Forum.
@Viz thanks for explaining that! This kind of info is very helpful.
Can skin pet Companion of War put in skin pet panther?, so there are no two panther if we want to choose pet.
Yeah, that is doable. In the next version, then.
which one of them is bugged? I can't do much if its related to animation
5 New Pets - Baneling (Starcraft), Gusting Grimoire (World of Warcraft), Treasure Goblin (Diablo 3) and Big Bad Voodoo (Diablo 3) by Gao. Very high quality new pets taken from Blizzard games, with nice textures and sound assets. Unfortunately for now these pets can't cast attack spells; I added them anyways because of their high quality. The author should have them fixed soon.
From Steam Torchlight II Essentials
But I hope this is better put into mod test. Because I'd rather if Mod Variant just focus for the class merges only
. So if you agree with my thoughts, what if Mod Mini gun, Flamethrower, & pets are included in Test Mod.
As I said in the forum "Some Bugs Report and Request Idea" :
What about combining Mod Torchlight II Essentials + Mod test [the old version (Evil UI Grittier Edition + Diablo 2 Orbs (v.6) + Skills Expansion + Alternate Outfits + spells redux (v.1) + TL1 Rifles (v.4) + stat(x10) + skill boost(x2/x4))].
Because, I see most of the mod that I want to combine already in Mod Torchlight II Essentials (just don't have: Mod Evil UI Grittier Edition + Diablo 2 Orbs (v.6) + Skills Expansion + spells redux (v.1) + TL 1 Rifles (v.4) + stat (x10) + skill boost (x2 / x4 )). Maybe it will not cause crashes, because Mod Torchlight II Essentials is already stable
Although there are pets that can not use spell attacks, I hope you can fix that bug.
Maybe you can name it: Mod
"Variant Essentials" 
I think if Variants Classes's merged with other mods, it should be new mod beside Variant Classes
Absolutely. Only a few of non-class mods are merged into Variant.
I don't want to turn it into Essential either.
@Viz will Variant keep unique behavior weapons such as Minigun, Flamethrower and TL1 Rifles?
Or will these be placed in their own unique weapon mod pack where further development of curious weapon options will continue?
Hmm I see no reason to separate them from Variant. So they stays.