The distance from the lens to the work is the focal point and that distance never changes. The extension tube and the nozzle are just to get the air assist close to the work and maintain the prescribed 10mm gap from the nozzle to the material for easy reference.
This mod will require you to manually focus to a calculated focal distance that you must determine and this mod will affect the air assist as the nozzle is far away from the material.
Do not use autofocus with this lens assembly or any other Thunder or aftermarket lens assembly! Autofocus is meant for the stock 2" head included with the machine only.
Here is more on that: Nova Series Overview - Heads, Optics, Focus
If you do crash your head here are some tips: Preventing & Recovering From A Head Crash
You can gain extra clearance for things like engraving the centers of platters without worrying about the head contacting the platter's taller edges, etc... by using and modifying the 4" head. You should gain 44.6mm (1.75") of clearance (plus the 10mm to the focal point minus 1mm for fudge factor) gives you a total of 53.6mm or 2.11 inches of total clearance when focused on the inner surface.
IMPORTANT: This head was designed specifically for cutting thicker substrates and was not designed for engraving. The spot size is larger and beam density is decreased so line interval and proper artwork and prep will be a factor. You basically cut the resolution in half with the 4" lens as opposed to the stock 2" lens.