Yup, I tweak guitars all the time.

A few years ago I bought two all mahogany acoustics, a Seagull dreadnought and an S&P folk size. I literally drove them from the store to the luthier's shop for aftermarket pickups, bone nuts and saddles, and fret dressings. Sure, they were acceptable as manufactured, but some refinement was left off for the sake of price (I suspect). They're better post tweak.

Many of my guitars, Josh House and Marc Beneteau guitars among others, have received my favourite machine heads, Gotoh 510s. One House has had a scalloped cutaway added, two soundports added then one filled in, refinish, refret, etc...it's been a huge ongoing experiment.

My little Kala tenor guitar had too twangy a tone for me but brass bridge pins added some mass to the bridge and smoothed out the tone considerably. The pins themselves sat a little too proud of the saddle so I milled a little off the head and polished them smooth.

I often tweak the depth/width of nut slots to accommodate action and string gauge.

Pickups in and out...I'm never happy.

One of my mandolins, a Moon, has a Weber tailpiece, Schaller machines, radiused body binding, cocobolo/bone solid bridge, none of it stock.

I could go on, but yeah, I tweak therefore I am.