I think that mma's smarts are getting in the way
But, for a simple bass line you'd probably do something like:
bass sequence {1 4 1 90; 3 4 5 90}
which as you've discovered will play the 1 and 5 on beats 1 and 3. So long as the chord is the same, it's all great. And, most of the time it sounds fine too, no matter how many chords there are in the bar.
But, for the occasional time you want something different, just use a RIFF. So, to continue the example above, just before the 2 chord bar insert:
Bass Riff {1 4 1 90; 3 4 1 90}
22 C / G /
Now, the notes played will be C and G, not C and D.
The RIFF just applies to the next bar.
BTW, I find that in my music I use the RIFFs very seldom to change patterns since the "standard" stuff sounds fine most of the time. However, I find that I use them more for changing the articulation and/or volume for special effects in parts like endings.
And you can make this much simple with either macros or using pre-defined patterns. If you are using a groove from the library (or by doing an Include stdpats) you could do the sequence def with:
Bass Sequence B13
and the riff as:
Bass Riff B11
Just saves a bit of typing.
Hope this helps.