You mean like Sky's original Seikan Hikou ust?
There's a fix to those spaces.... in a program that can slice audio clips, however.
Split/slice the clip at the off time bits and move the second part of the sliced audio to where it would be on time. o_o If this happens in between notes however, that's plain weird. I would hate slicing those up.
I had to do that for Mr. Munou's Hidalgo UST, as it's off-time, even in normal notes. Some of them are too long, some of them are just right but the rests are off. o_o
And guess what? Now I want to make a on-time Hidalgo ust, because DAMN I HATE THAT UST.