FWIW this is also why I never bothered with all the diffserv tinkering. If you have very low bandwidth (say, a couple of megabits), and use applications that tend to continuously use lots of bandwidth that you want to throttle in favour of other traffic (say, bittorrent or cloud backups or something like that), the diffserv-based marking can make sense. But if you don't do any of these, the flow queueing will generally be enough to get you excellent performance on its own.
As for your other question:
I think it might be fine with that, actually? sch_cake itself uses the skb network_header offset and the kernel flow dissector to retrieve the DSCP marking and distinguish flows (respectively), and both of these should deal gracefully with a packet with no MAC header. The simple way to test this is to just look at the cake stats and see if they look sane (i.e., packets are hitting the tins you expect and flow counters are going up). Which it looks like you've done, so yeah, I guess it's working? 