There is a cause for {under,over}runs ;). You already mentioned the
right term, the so called "bottleneck" :D.
Unfortunately the "bottleneck" doesn't show up by a blinking LED or
something else.
I didn't compare the current lowlatency Ubuntu kernels with my
rt-patched kernels.
An rt-patched kernel could improve latency a little bit. It's my first
finished week I worked full-time, after being "free", independent of
uncool time management :D. However, assumed you shouldn't know or be
able how to find out, how to build a Debian/Ubuntu package for an
rt-patched kernel, I'm willing to help you next weekend. I've build the
kernel-rt a thousand times, before I migrated to Arch Linux.
Sometimes > 48 KHz is used to reduce latency, but regarding best audio
quality, you only need 48 KHz.
If I would be you, I first would try to use an rt-patched kernel at 96
KHz, as well as 48 KHZ.