That's not a "flat spot" per se.
A flat spot would be if your school boy in 2nd gear stopped for a little while between say 3000-3200rpm before going hard again. That would be a flat spot.
What you're doing is underloading the engine. To see even the middle top of 5th in my car you're doing around 250kmh+ so if you whip out 5th and it isn't down the hill and you're doing 80 you're not going to have the response when you're in boost in 3rd.
That's really not it. See above. If it WAS exhaust restriction it would be RPM dependant and it would be a gradual curve/taper in restriction. This is because the restriction would be directly relative to the volumetric output of the engine at that RPM/load. So you wouldn't experience this as a flat spot, unless for some reason your exhaust was changing in diameter as you accelerated.
By your description in your first post it seems normal - if you're worried get on a mountain/racing bike and see what happens when you pedal at a low gear, then at the same speed click it into the highest gear. When you pedal at this point you'll notice you're expending more effort to move the bike - that's the same thing.
Either way a good exhaust will free your engine anyway