The real difference between 95 holy weapon and 90 dod weapon is the matk / patk, but for classes that are matk patk reliant such as Mecha, DB, HB, GM, Blade Master, Celestial Arrow, Annihilator and others would use the 95 holy weapons, yeah some regular trial 95 weapons are better than the 95 holy ones but from a new player standpoint i'm sure that most would prefer to do Lv95 DoDs to get weapons fast as it only requires 2 Godstones as appose to DoD's 10. It's true that the 90 weapons may not need to have the 95 holy skills on them but how would most people test the skills out before commiting to a class? Yes you can read them from Goddess' post but some things may sound strong or weak but when you try them out they're pretty good. As an Annihilator and Mecha main in this current patch I can vouch that all 3 guns are good, Lv95 from Trials and the two from 95 DOD. But in my eyes the best gun is the Buck shot one. And for Mecha, the best for me is overdrive due to what it gives, it's pretty great. The 95 regular one gives you 5% more base matk but who cares about that when you're getting more damage? At the end of the day it comes down to time, if you have the time or not lazy to run the 95 dods, but I think what sets people apart is wanting BiS( Best in slot ) equipment or just lazy. I'm a lazy person but I'll always go for BiS stuff.
Doesn't work with some stuff, like the Overdrive skill on mecha. Unless i'm doing something wrong but when I activate the skill on the 95 holy weapon and swap guns I get into the debuff state. I'm sure that was intentional to prevent people from exploiting swapping to a certain degree