Wilfred,
While I'm not Alembic, here's my two cents:
1) It will probably be no cost, or maybe even a credit UNLESS they absolutely need the slightly extra depth the accent lam provides to be there;
2) Adding a filter to an instrument that doesn't have one will cost you. My Orion has the EMW package that, basically, takes the standard Orion Package and just adds a filter with Q switch. That addition added $650.
3) There is one Custom Orion that I am aware of that I saw somewhere here on the site. I think it's in the Custom of the Month archive, but I couldn't find it the last time I looked for it. Unlike my Orion, which just has Purpleheart stringers (i.,e, accent stripes or thin lams)instead of the standard Walnut items, this one had actual thick lams like a neck-through instrument. I can't remember if they were Ebony or PH (the latter is more likely). This instrument also had a bridge block (I didn't realize I could get either option, so I didn't order both).
Personally, I can't vouch for the electronics package, having never experienced an Elan. As you are aware, I dig Orions, so you probably can't go wrong with anything you do. The accent lam thing is a personal preference item, so I can't comment on that either.
I'm in agreement that Alembic needs to upgrade the quote engine to encompass ALL the models, including guitars, and more options need to be included. This would cut down on Mica and Susan's email considerably, LOL!