In your Rank Tracker, each keyword/location pairing counts as a separate keyword. As always, you can pull rankings for multiple search engines with each keyword/location pairing.
Let's say that you're tracking the following keywords with the following locations and search engines:
In this example, you've got 3 keywords, each tracking 3 locations, and each keyword/location pairing tracking 4 search engines.
The number of keywords counted against your account allotment would 3 keywords * 3 locations = 9 total keyword/location pairings (Search engines do not factor into the calculation).
Connecting multiple Google My Business pages has no bearing on your keyword limit, and is not counted toward the limit in any way.