Hi,
This being a consumer forum we are not privy to Apple's reasons for its software designs. The 16:9 aspect ratio is widely popular and displays well on widescreen TVs.
As you have observed, iMovie 10's aspect ratio is set to 16:9, that cannot be changed. Vid clips with other aspect ratios either will have black bars or be cropped to fit the 16:9 iMovie screen. It would be nice if one could adjust the aspect ratio on export, like in iMovie 9.
There are a few tricks that can be done to accommodate some other aspect ratios.
One way is the one you mentioned -- to export the project and record the screen using the Command-Shift-5 feature to crop out the black bars at your desired aspect ratio.
Another way, when dealing with a vertical iPhone vid at 9:16 aspect ratio, is to use the crop tool rotation controls to rotate the clip sideways to fill the 16:9 screen. Then export it sideways and use QuickTimePlayer to rotate it right side up. That will eliminate the black bars.
A third way is to use the App Preview function in iMovie. Go to the Project Browser screen (where your projects are displayed as icons) and do File/New App Preview. A screen will open that looks like an ordinary project screen, except that it will have a few less features. Put in a 9:16 iPhone vertical clip or a 4:3 clip. Then export it as an App Preview (a specific option in the export box). The resulting export will not have black bars. I tried exporting with a square aspect ratio, and it did have some black bars. So apparently it might only work with 9:16 and 4:3 aspect ratio clips.
As for more customized aspect ratios, it would be necessary to use the screen recording crop method that you described.
-- Rich