Disclaimer - I have not worked out an elegant solution either! So I am hoping for some best practices...
I keep my lighter-weight anchor (fortress) in the locker - mainly used for a lunch hook. Like you, the main anchor/chain goes down the bow vent. I spliced the rope to the chain, so it does not foul. With so many other projects on your plate, I would go for the splice, and work out a better solution later. It aint't pretty, but it works.