These are valid concerns, but I would also like to point out Tesla's policy seems to be evolving. About 2-3 months ago when I took my Roadster in for service, the service center asked me to sign a 3rd Party of Aftermarket Accessory Waiver (or something to that extent). I wish I kept a copy, but the gist was that Tesla would work on cars with 3rd party accessories (I have a few on my Roadster - subwoofer, stereo, back up camera, dash cam, OVMS, smartphone mount, lightening cable in place of dock connector, powder coated wheels), but Tesla reserved the right to remove or disconnect any accessories if it was required for their repair. Again, I don't have the exact wording, but they certainly seemed to acknowledge many owners now have non-OEM parts and accessories and were willing to work around them.
A CHAdeMO/JdeMO is, of course, potentially a whole new beast, but if done well and professionally (and I expect nothing less from Tony), I imagine a knowledgeable owner with a good relationship with the service center could come to a mutual service understanding. No guarantees, of course, and there is certainly some risk, but the cost-benefit of CHAdeMO charging for $3000 vs a new battery for $29,000 might be well worth it for many owners' typical driving needs.
I'll be following this closely.