[@Gun]Thanks; glad you stopped by! 

To answer your question - certainly! I'm going to assume that our pilots have tinkered with their machines to make them as user-friendly as possible. Modifications here and there are to be expected and can be included in an extra section of the character/FRAME sheets. Internal calibrations to increase a pilot's familiarity with his/her machine sort of falls outside the realm of the customization mechanics I was working on, but can be assumed for all pilots.  
The customization mechanic mostly deals with chassis parts, weaponry, extra systems (engines, boosters, better radar/targeting computers, etc.) and other bells and whistles.  

Not sure if that answers your question; Did you have something in particular in mind?