Well there are two reasons why some do them separate. First there is the licensing issues, which rather than discussing them myself, I will link to an article about them.
Google Apps - RootzWiki
Secondly, it saves you from having to download them everytime the ROM updates. For example, if you were on ICS, the Gapps on Goo-IM, which quite a few ROMs use was last updated 4/29. So no need to download 50+MB of what would be wasted bandwidth every time your ROM updated. Or if you are a crack flasher, you can swap ROMs without having to download Gapps. With capped plans in the future, 50+MB is quite a bit. If a ROM updates quite often, then, that can become a problem. Also, as a ROM dev, this saves you from having to upload as much.
My opinion, I probably would lean toward separate due to the fact that Gapps for some ROMs are 80+MB. When a new ROM release comes out, and their server is getting hit hard, those extra 80MB make the download that much longer.
Glad to see you back developing. I enjoyed your work on the OG Droid and look forward to your GN offerings.