I'm just curious, what aspects do you think the 1DX3 will excel over the R3? Side note, from a marketing and PR perspective it would make sense for Canon to NOT consider the R3 a flagship without knowing how it's received by the market. It would be quite the blow to Canon as a company to consider a camera a flagship and it not perform. But if this camera excels past the 1DX3 in just about every fashion and is widely received by the 1DX community, what would make you think the R3 would not eventually be considered Canon's flagship, even if "unofficially"?
Mechanical FPS is one area the 1DX Mk 3 may still be ahead, AF accuracy (as it has cross type AF and no mirrorless has this yet), we already know it had dual CF Express and the R3 only has one CF Express, perhaps even build quality.
The R3 is going to be pretty much the best mirrorless camera you can buy until we see the Nikon Z9 that may or may not surpass it. No one will be disappointed by a R3, but a 1DX Mk3 user is likely still going to want to use that. Though my opinion and your's is irrelevant here, Canon have made it clear that the R3 is not the R1 and is not here to unseat the 1DX Mk 3 and you can be sure they'll make it so. Already it falls short by only having one CF Express slot.