Hi James, I think the order you do things might depend a little on what technology you have available to you. It would be possible to rout or laser cut a shallow engraved pattern into a layer of constructional veneer (1mm+) so that you could fill it before you laminate it. The technique options open to you for this type of inlay after lamination would have to be largely performed by hand and strike me as likely being a massive pain in the ass!!
If you just want a pretty inlay strip down the centre join then this is definitely done before lamination and damn convention, if you want one, its your guitar, put one in! Maccaferri never used them but it didn’t stop me and I really doubt that Mario is spinning in his grave!
Cheers
Darren