Yes you can probably pad them out (3D print is an interesting idea!) to fit a 40mm holder.
However, the problem I’ve had when I tried that (I just used tape to fatten the neck), is that with the Sky LNBs I used, the 37mm bit of the neck is very short. Once the centre one is in the dish’s holder, there’s no room for the multi LNB bracket to slot round the tiny bit of 37mm neck left - the part of the neck further back is much thicker (thicker than 40mm too). Then to line up the other LNBs, the adapter has to fit round their necks at a similar point for them to sit far enough forward.
Whatever I tried on my Zone 2, I ended up reverting to cable ties for 13°E and 19°E with two sky LNBs after a short time. Now I’ve switched to three 40mm Inverto Ecos for 28.2E/19.2E/13E which work fine with the multi bracket and I have a lot less grief with things coming loose!