There is certainly no harm in vanishing those areas. It's a bit more protection against water intrusion. But I see no reason to do a neat or careful job in an area that goes unseen. Apart from water protection, the varnish is unnecessary sunscreen in these areas.

after a lot of boats and refnishining and repairs, my recommendation is if there is no sun exposure, don't varnish it.

the basic reason for this is if you ever need to do a repair or you want to add a fitting you didn't anticipate, you now have to remove the varnish because you can't put epoxy over varnish.

so my perspective is the application of varnish just creates a more complex situation to sort out vs straight epoxy....therefore only use it where it is needed.

h