The issue of aftermarket bags hitting or interfering with the stock rear turn signals is one many have faced. Personally, my solution was to simply replace the stock signals with shorter/low profile signals (see photos). I currently have Viking bags on my VTX, as seen in the bottom most photo, but I have a custom plate the bags are mounted to that holds them out from the bike.
To me, this is the best solution that allows your aftermarket bags and also allows fender mounted signals so you don't have holes to fill. Viking bags sells a quick disconnect system that holds your bags away from the fender some:
Viking Saddlebags Quick Disconnect System For Honda VTX
I suggest you take measurements of how much clearance you'll have after your bags are mounted and then order a set of signals low enough to clear the bags.
Here is a link to where you can buy low profile quality signals:
Featured - LED Signal Lights
Some have opted to order license plate holders with the integrated signals built into them, but then you have fender holes to fill.
