The justification is you do it because you want to and if that makes you happy that is the only justification you need
I have always been a modder so I like making guitars to what I want them to be. I just like. They don't stay stock for very long. I replaced TRC, pickups, bridge and TP on my Trad + pretty much right away. The only time I don't tinker is if it is a custom built guitar to my specs.
I do question some folks who mod where it really doesn't make financial sense (in my opinion anyway). For me it doesn't make sense buying a Studio and spending $500-700 modding when they should have used that money and move up once class and bought a better model to begin with...but hey, whatever makes you happy!