I've had a kemper a while and really love it. When I first bought it, I tried it in several configurations to find the optimal setup.
I'm using it with a UAD Apollo (1st gen), which is by no means a top of the range interface - that said, using the JFET DI instead of the kemper's input is a very noticeable improvement (extended range/clarity, more realistic feel, exactly the difference I experience between different DI boxes). I'm going in and out of the kemper via SPDIF which is nice as it saves my analogue inputs/outputs for other things and presumably the conversion in the Apollo will be better than the Kemper's.
There is definitely a difference in the sound of the D/A of the Apollo when I make the kemper the master clock. I had never previously noticed as drastic change in the sound of the D/A when changing the clock (I have a few ADAT preamps that I've run as the master before), so it seems the clock in the kemper is definitely something that could do with some improvements too. It'd be great to be able to run it as a slave, and also at other sample rates (although the Apollo does have an option on the SPDIF inputs to convert the sample rate).
It definitely makes me curious to try some other DI boxes with the kemper - I don't feel any one DI box will be perfect for every guitar and bass, and I'm sure there are better options out there than the Apollo. I'll most likely pick an RNDI up further down the line as I can make direct profiles of amps with that too....