Yes Attack pattern Alpha is the only stackable pattern as its a captain power, by making it unstackable with the other 3 it will reduce the burst damage some but not by a huge extent.
The other non alpha attack patterns go on global cooldown cause they on the same system such as every other BO power is tied to a specific system. captain powers were removed from the global cooldown system.
With patterns on a toggle a tact captain can still do burst with their other cap powers just not as strong as before as they can't stack omega or beta onto their alpha anymore. However with their patterns on toggles they can keep the buff going much longer increasing their sustain damage potential over longer periods of time. Another plus is they wouldn't need more then one copy of a particular pattern freeing up tact BO spots for other stuff. The main abvantage would be for sci and eng captains that don't got the burst tacts do so they are more competent at burning down their targets. Another benefit is you can use only the pattern you current need and not have to bother with rotations to fill in gaps.
So if you wanted to escape or chase down a target you use omega.
If you or a teammate were being focused on your hit delta.
Once the shields go down you can go beta for extra hull killing or to support others using alpha or omega at the time.
I've been toying with the idea for team wide benefits for the existing team abilities to make getting the higher ranks more tasty options. This is just the rudimentary concept I been working on. Like with Tactical Team
Rank 1 - Is as it is now.
Rank 2 - provides the buff to both you and a selected friendly target, maybe will share your current pattern to you friendly target for the duration of buff.
Rank 3 - would share the buff to all allies in 3-5km of both you and your target but only the skill portion, maybe share the current pattern buff to all effected as well.