Any dyno runs I have seen for a stock R100 GS has shown a dip between 2800 and about 3500 revs.
If the bike is in fine tune it is much less noticeable but it is still there.
It is possible that the Y piece will upset your fine tune making the dip more noticeable again.
It is also possible that the Y piece improves things outside the flat spot , making it more noticeable.
It is also possible that the thin aluminium gaskets between the various pipe can fall apart, and the bits partially block the inlet to the muffler - like mine did.
I always seem to do more than one thing at a time when I work on the bike , so I cant be certain what did what, but after fitting the Y piece it was not good.
I checked and set everything, fuel level , plugs , timing, carb balance, etc to no avail . Then I noticed the heat band round the muffler at the intake position.
The muffler was removed , most of the bits of the old aluminium fell out but there was a large piece which was still rattling around inside.
I enlarged the small inlet hole out to 1/2 " but it still wouldn't come out, so I resorted to to the 1970s schoolboys tuning trick and tried to knock a hole in the baffle at the back of the silencer with a sharpened steel rod .
Success - the back baffle bent over and a large, fused lump of aluminium fell out. I hooked the baffle back a bit straighter ,but there was still a decent gap at the edge.
To complete the schoolboy tuning I unclipped the snorkels from the air box.
Eureka - the flat spot was gone , there engine is much livelier all the way through but especially over 4500 revs , there is a pleasing burble from the exhaust and fuel consumption has decreased slightly.
FWIW there was an article somewhere where the muffler was replaced with a Supertrapp, the snorkels removed and the carbs tuned , and they got good results on the dyno - 5% power increase and and more than 5% decrease in consumption. They had started with a lean tuned US spec motor , so a European spec PD may not replicate the results.
They started with around 71 hp and ended up with nearer 75 - let us know how you go.