Date of employment, for the record: May 2, 2005.
Man, if shimming a bolt on neck to achieve ultra-low action is an "extensive aftermarket" modification, well.....
I've had to do this to so many bolt on necks over the years from Fender to Fodera that it's just a non-issue to me. We do make every attempt to set the action as low as reasonably possible before it leaves the shop. Keith is primarily a guitarist, and actually I end up asking him to bump the action UP more often than anything else, because with my ham-handed bassist's techinque, it just gets buzzy to me.
Further, we haven't changed our bridge design, and I AGREE with Keith, it makes total sense to me. There are far too many negatives to having the saddles sitting at the top of their excursion, and too many positives to have it very low if not sitting ON the bridge plate for it to be a "design flaw". I understand that there may be a difference in philosophy, and that's fine, but calling it a "flaw" is pretty silly. That said, we are trying to be more conscious of leaving a bit of room below the saddle to allow for those that have a more extreme idea of what "low action" is.
Oh, and for the record, my primary bass for the past 5+ years has been a Zon Sonus Special Fretless 5 string. I'm sorry, it's a great bass, but I know I can get my fretless Century set up lower, because I have.
Oh and, no knock on the Zon, but guess what, I shimmed the neck in my Zon, and didn't in my Roscoe!

Folks, bolt on necks are NOT perfect every time, no builder that does them is 100% perfect in my experience, from
Azola to
Zon (and yes, I do know what I'm talking about, after 5 years at Bass Central).