Ok, basialy if I get this right, any instruments would be able to "take" Down tuning with the right tenssion.

Following this guide:

if I currently have, lets say, an RG350 (Floating bridge, 25.5 scale), go from standard tuning using an EXL110 (10-46 stings) , change them for a kit of EXL156 and tune it in Baritone (B tuning, 3 step down) it should take it "just as well".

Surely, I'd have to adjust the spring tension, intonation, would I have to adjust the truss rod also?

Anyone can tell me if that would cause any issue on the long term?

Probably not the truss rod.

But yea. The baritone set works fine.
Original 1969 Fender Jazzmaster
Jackson JS32R Dinky "Curry"
Jackson Stars Kelly "Aiko"
Ormsby SX6 prototype
Dingwall NG-2 "Kimmy"
MiM Fender Jazz Bass "Pancho"
EVH 5153
Should work just fine, probably won't need a truss rod adjustment, but if your not comfortable with setting it up just bring it to a good tech to take care of and you should be good to go.