I know it sounds crazy, but I have gone to almost always using an roughly 6" piece of 3/8ID silicone tubing. I simply slip it over the end of my tap, which coincidentally makes it almost the exact diameter of the mouth of a beer bottle. I make sure the bottle is wet and cold, dial down my regulator to ~3-4PSI and fill. It foams a little bit, but I just let the foam burp the cap for a second or two and then seal it.
I did the Cobra-tap/racking cane/stopper system for a while, but after doing the above system on growlers, I realized I could do it on bottled as well. The trick is to use the thick silicone tubing and it creates a counter pressure seal, you just fill slow and burp it as you go.
P.S. If you have intertap faucets like me, the barbed tip works even better.