I think Phil has my notes on this but I'll throw this out there for entertainment.
Theoretically, increases in braking performance from the ABSII lever/caliper combo will probably be lost by the disc smaller diameter having less leverage to stop the bike.
If power equals the ability to lock up the wheels, then there is no difference between the standard an ABSII. Opinion based on many miles of riding both ST1100 models.
But, realistically, the way the input from your hand lever is applied by the system results in a quicker response with less effort from your hand because there is the secondary master cylinder adding braking power to the effort from your hand.
The initial feeling of switching from standard to ABSII is that the ABSII stops a whole lot faster.
Once I ramp up hand effort I'll reach the same amount of braking power. During that ramp up in effort difference between standard ABSII there has to be some difference in stopping distance even the braking power is ultimately the same, the ability to lock up the wheels. That difference in distance might be inches or could be feet depending on how well attuned one is to the bike.
My other experience with linked and not linked is with the VFR800 and ST1300.
Delinking the VFR and plumbing to all six front caliper pistons resulted in way too much travel. Since I drilled the calipers I got a CBR600Fsomething master cylinder to make the piston ratios the same as the stock VFR lever plumbed to the original four outer pistons.
It brought up the consideration of what variable modulates stopping a bike, brake lever travel distance (very little change in effort) vs stopping with hand effort increase (very little change in lever travel).
Somewhere there is a balance.
With the ST1300 I went straight to simply removing the plumbing to the center pistons. (rear gets all three plumbed together)
The difference between the linked and unlinked 1300 is similar to the difference between the standard and ABSII 1100.
Based on the VFR experience, I want to test plumbing in one front center piston on the 1300 to see if that balances the ratios more favorably or not.
Phil, I figure you'll find 6 piston too much.
It will be interesting to see if 5 works better.
If 5 is too much it would be certainty be better than 6.
Also if 5 pistons is too much with the ABSII master cylinder, then using the standard master would put the ratios in the right direction.
Although some combination above might work better or not, using four pistons with the ABSII master is going to work fine.
Now if capping the center pistons turns out to be the solution, it is standard procedure in the land of delinked VFRs and Blackbirds to drill a small hole in the bleeder so there is no chance of air expanding and pushing on the piston.
And this is what happens when I run out of