Hi Aaron. That’s right, and comments too.
Well I thought the whole point of the Boiler plate was to produce sites using good, valid HTML5. If you allow those tags then the Boilerplate will have created pages that won’t validate. Comments already don’t allow, say, font tags, so adding a couple more makes perfect sense to me.
Developers / editors may not not be familiar with the difference between HTML5 and 4, so a bit of help may be needed.
Changing acronym to abbr and strike to del (I assume those are the modern equivalents you are referring to) would indeed be more friendly, but much more involved. I suppose that would make sense for you, as you are distributing a theme for general use.