I have a Kona 3 card and I'm using it in Motion to do graphics for a upcoming series that we are working on. Now, my experience with Motion is rather limited but I do know that Motion and AJA have preview support.
In the preferences for Motion, you can set your Output type. AJA gives us all the screen resolutions needed for preview output BUT they don't gives us codec specific screen resolutions. I work primarily with DVCProHD (which is 1280x1080) and the AJA screen settings are for 1080i60 (which is 1920x1080), therefore, my project preview output looks really squished because I'm seeing 1280x1080 outputting to 1920x1080.
Is there a way that I can work entirely in DVCProHD and view DVCProHD preview?
When previewing through my Kona, Motion always seems to be sending out square pixels, so your anamorphic comp looks squished. My workaround is to make my comp a square pixel, 16X9 comp at either 1280X720 or 1920X1080, and work that way.
I don't really bother with that extra step. Either I bring the square pixel comp into my FCP timeline & render it there, or I export it as DVCPro HD. I haven't had any problems with the square to anamorphic pixel change.