The only way out of Motion with alpha is ProRes 4444 (or 4444 XQ) and the transparent parts are going to look a little weird (in many cases - "not there") when you play the movie all by itself. The only way to tell if there are actual differences is to overlay the video on top of something else (image/video) and see if you get the results you intended.
If you're used to other applications (like Photoshop) that allows you to "premultiply alpha" — that is actually a technique where the application adds a "bias" to the areas of partial transparency with the anticipation that the blending those regions against a similar type "background" (typically, the premultiplied alpha is against either black or white). There is no option to premultiply the alpha from Motion (or FCPX) — it is completely neutral.
That said, there are (older) filters (like the glows) that are not the highest quality rendered with alpha. For Glows, the best one (and newest) is Glint (it can be adapted to a general glow type without the anamorphic streaks.) So there are a few things in Motion that might make the transparency look ... off.
If you are creating your designs in Motion, but using Final Cut in your editing process... then the absolute best method is to simply publish your design projects as Generators for Final Cut Pro. Motion automatically saves them where FCPX can find them, and you can publish the parameters that directly concern the alpha/transparency aspects so that they can be fine tuned in your editor (FCPX). Since all Motion projects are a form of XML (text only), that is an immensely HUGE savings in the memory used for the project.
HTH
