Don't worry about it. Most of the old ones I have taken apart & seen apart were built this way. The first couple I built I did the same cause I thought it was the way it was supposed to be. Now I don't do it that way because it causes a cleaning issue.
So.......
DO NOT try to drill thru the barrel & drill part of the breechplug edge out. That will be a disaster & you will end up with a oblong hole & only half the required threads you need to safely secure the vent liner. With the 5/16" liner of a B weight barrel, you don't have any room now for a screwup. If you have not drilled it at all, I suggest ya go with a 1/4" vent liner just in case you do make a mistake, you can always go up 1 size to remedy it. Also if you put that 5/16 vent liner in a small bore, you will feel it every time the jag gets to that vent liner hole. If you use a 5/16 vent liner you also need a larger groove in the breechplug face, so if you have not drilled yet, I would go with a 1/4" vent liner. That being said..........
Take the breechplug out of the barrel, lay it beside the barrel with the tang edge up against the bottom barrel flat & positioned exactly like the plug was in the barrel, but against the bottom flat just as it was installed. Take a marker & mark on the breechplug, like the hole is in the barrel. I put a straight edcge across them so I don't mark out too much on the plug. Now grind that out & take a thread file & clean up a little & go back in with the plug & see how the clearance is. Remove & take a lil more if necessary. I suggest taking a dremel & polishing that groove with some polishing rouge & get it shiney & slick as I could.
You will most likely have to shorten the vent liner a tad so you get it in all the way.
As far as cleaning the groove, you won't be cleaning it very well. You may flush it but I have seen nothing yet that will clean it good, other than a bore brush from MBS does fairly good on one. Kinda like cleaning your car in a brushless car wash. It may clean off the top coat of dirt & dust, but the scum is still there. A bore brush from MBS is the only thing I know what will get into that lil groove pretty good & they don't hold up too well if you put pressure on them to get into that groove.. Most guys clean them the best they can or call it clean anyway & never admit about the fact they cannot get a patch into that groove. And flushing it doesn't mean it is clean, maybe the most of it gone but not clean down to barel metal.
But even at that, if you get it flushed out good & dry & a rust inhibitor in it, you will be OK & the barrel will outlast you & several others.
Good Luck !