You are correct that Vault will not handle that particular scenario very well (at least the part where you have to retype out the job number. Your cheapest bet will be to try what swalton suggested in your earlier thread
here, although it isn't a very elegant solution, it would let you use any old batch file renaming utility. Depending on how your file structure is set up Inventor may or may not auto-find the proper directory for you to pick the found file when it tries to repair itself so you may not gain time on that.
I don't know how many of these templated assemblies you have, but it may also just be more financially beneficial to create the jobless -123 part numbers and then use Vault to rename them and add the prefix (because it will do that). Yes you'd have to do the renumbering for the first batch, but then you can copy design in Vault to take care of any future ones. You wouldn't even have to set up a central Vault if you don't want to. You could just use a local one.
An add-in wouldn't be too tough to develop for this particular narrow application as long as you want it to do exactly this thing, no more, no less. It might take a few weeks including bug testing. You'd just have to crawl the leaf occurrences of an open assembly and do a save / replace on them. There might be a few more complications than that, but most of the code to do this is already in the SDK samples of 2009.
I don't know how Autodesk does things exactly, but you will probably get a more direct response if you go through your value added reseller instead of just throwing a question out into a forum. I'd go out on a limb and say that having a custom add-in (even such a simple one), will cost some money though. There is real time and effort put into such things.
I'm also going to put my own personal caveat in here about developing add-ins and macros: It is much better to have these types of things done in house. Whether you have them done in-house or or shop them out, insist on having full source code backups and documentation. Also, although you may have a fancy button to do something, make sure you have a backup procedure for people to fall back on because somewhere down the line, they may break.
You upgrade to a new version, move to Windows 2015, whatever. Something happens and it doesn't work and you need to make sure that all of the draftspeople that are there when that happens know how to function without it. With any luck the source code and documentation will help whoever is in charge at that point to get it fixed more easily as well.