I want to apply Replaygain all at once using the album setting to a very large folder where 90% of the songs have album tags. I'm worried about what will happen the songs without album tags. Will any value be calculated?

Don't want to have to outsort them all first if I don't have to.

In foobar2000, you could sort by album and then remove the ones without album tags from the playlist. Then apply album Replaygain. Or you could add album Replaygain by directories (you may have to put that option into your context menu first).