I was thinking about doing Equipment Extensions on my Atlas but then I read the disadvantage of doing that...

https://pso2.arks-visiphone.com/wiki/Equipment_Extension

Apparently I'll lose the bonus class equip permissions and innate PAs and while I don't understand what that means exactly, but it sounds like that doing so will make my weapon weaker instead and will not gain any of the benefits of a class boosting its power. So now I'm wondering if it's worth upgrading my Atlas to keep up with the new weapons or not outside of affixing.

If you can't find a weapon that's meant to be used all-class/etc. then you might as well not use it for the classes it's not meant to be used on. The only all-class harmonizer, for instance, is only obtainable in Tokyo Rainbow right now, and even if you do get it, you still need Summoner on sub-class to use its pet PAs, at least last I checked.

(Also Harmonizers cannot be extended or crafted.)

@coldreactive I just want to make my sword stronger, but that extension is better off with the Occuld Series, the series where any class can use it? Well I guess it makes sense, since it is the weaker of the swords...

@Guilrel Weapon extension is only for 13 star rarity weapons or lower, its purpose is to allow lower rarity weapons to get closer to the power of the higher rarity weapons.

Also the link in your first post is for the JP version, check this one for the EN version:

https://pso2na.arks-visiphone.com/wiki/Equipment_Extension

I'll elaborate a bit, let's use the Sigma Bastad (launcher) its All class & can use Divine Launcher regardless of class. The "bonus class equip permissions" refers to every class that can't equip Launcher, so if Extended it will only be equippable by Ranger.

The "innate PA" here refers to Divine Launcher, so you won't be able to use that PA with it unless you're Main or Sub Ranger.

While Extending there is a chance during Great Success to add a class or 2 back & sometimes all.

Lastly the highest power of an extended weapon is about slightly under Ophistia's +35 Power.

I'll note though that the (Sword) Occuld Diene+35 - 2173 | Extended Sword+35 - 2215 | Ophistia Calibur+35 - 2303

Additionally regarding the Millioraj Dusk (All-class Harmonizer) it has dropped in Disturbing Whistle of Chaos on UH, so not solely Rainbow Keys.

You got a misunderstanding of the equipment extension system as those 14/15 star you listed cant even be extended - and at this point of the game, it is not worth the investment you need to put into it to extending equipment

@HarmlessSyan @Church10129 Thanks for the explanation guys. I just felt like I should probably do something with all the low level materials I've been gathering. Especially since Luminmech seems to be an increasing viable material that most would grind for now.

Honestly, weapon extension was added to Global LONG after it was even remotely useful. It's a dead feature and more or less has no use beyond around Episode 4.