Dear, it may decrease the resale value to some extent as you are cutting a part of roof.
But don't worry, it all depends upon the buyer.
I will always prefer a car which is mechanically sound not physically.
I have seen a lot of car fully repainted selling easily in the market, so I don't think you will face any problem while selling it.
Infact, you may get some good offers considering a rare Vitz with Sunroof.
Last but not the least, you like it so don't hesitate,go for it.
"Apna Shouk pura karo yaar, chaar din ki zindagi he"