FWIW, I believe the original (Silver) Apollo is actually running Firewire protocol over Thunderbolt.
IOW, It's not running "PCIe via Thunderbolt"... which is necessary for PCIe level performance.
I've got the Apollo-8 here... and it's just fine with CbB.
If you're after lowest possible round-trip latency, that's not the Apollo-8/16's forte'.
The onboard "Unison" processing is a great feature... but it comes at the expense of slightly higher RTL.
Of course, if you'll never monitor Native EFX via software, it's certainly worth the trade-off.
Using the Apollo-8 at 96k, the smallest ASIO buffer size is 64-samples.
Running moderate loads of native and UAD plugins, you have to raise the ASIO buffer size to 128 or 256 samples (to avoid pops/ticks). Same project running with Quantum (set to 32-sample ASIO buffer size) is completely glitch-free.
If you want to do things like run Helix Native at higher sample-rates... with ~1ms total round-trip latency, Quantum is one of the best choices. It's absolutely rock-solid.
The only downside to Quantum is that there's zero DSP for onboard hardware monitoring/routing.
It has to be done via software (you have to open your DAW application to route/monitor).
A workaround is to use something like the Presonus Monitor Station 2.
Say you've got a guitar processor like the Axe-FX or Helix Floor.
You could connect the Axe/Helix to your audio interface via S/PDIF... and route the analog outputs to Monitor Station.
You could then play the Axe/Helix thru your monitor speakers... without having to fire up the DAW.
Presonus deserves serious kudos for Quantum.
By far the best audio interface they've released.