On the other hand, maybe Canon has data that shows that starting over with a new system is not a huge barrier for people who are progressing up the chain. We may all be way overestimating the value of an imagined upgrade path.
That's where I'm placing my bet. I imagine that upgrade path as linear, in part because that was my own path – APS-C DSLR with EF-S lens, then adding some EF lenses of longer focal lengths, then getting a FF DSLR for which I already had some lenses. In theory, that made my decision to purchase a FF body easier, but in reality I was looking to increase my image-making potential so I probably wold have ended up with a FF body regardless. It's the same reason I swapped my EF 85/1.8 (the second lens I bought for my T1i/500D, after the EF-S 17-55/2.8) for an 85/1.2L II.
Canon knows how many APS-C owners who buy their first FF DSLR buy the kit lens (e.g. 24-105/4L) with it. I'm guessing it's a high proportion. They also know how many people who move from APS-C to FF had EF (vs. EF-S) lenses. Those who bought a 2-lens APS-C kit (18-55 / 55-250) would have to replace their entire kit anyway, much like anyone moving from EOS M to EOS R.
It's also important to remember that for the time being, there are two 'camps' of people who may buy an R-series body – those currently using a DSLR kit, and those using an EOS M. Given the market data, it's fair to say that the former camp is much larger than the latter (because DSLRs are not too far behind MILCs in the current market, DSLRs were the majority of ILCs until a few years ago, and there's a big historical installed user base of DLSR). For those folks, Canon has provided an easy upgrade path in that all their lenses, EF and EF-S, will mount on an R-series body with a simple adapter.
I also agree with your point that Canon is pushing toward a third 'camp' – making a FF MILC a viable entry level option. They've got the (relatively) inexpensive lenses, and if they bring out that rumored <$800 FF R-series body, they'll be in the game. Consider that an $800 EOS R with the RF 24-105 non-L would be $1200, and the EOS M6 II with 15-45mm lens and EVF retails for $1100.