I have always primed damaged areas with an oil base primer, Kilz or Cover Stain, allow to dry for a few hours then do the mudding. This works fairly well with little or no bubbling. One thing; make sure to saturate the paper and especially any open (exposed) sheetrock. Plus give it time to fully dry, coat it too soon and there will be bubbles.
What sealers have you tried? Water based primers will always cause some bubbling. I also use setting mud, typically 45 minute but do use 20 minute for small patches. I think the setting mud (powdered) works better than all-purpose.