I think you're confusing several topics into one question
In your title, you're positing Big Sur and Catalina being installed on an external versus an internal disk. I don't see what the comparison/contrast would be of external and internal drives and why it would be an issue installing either operating system on either drive. I suspect you mean to ask about Catalina being on an internal drive and Big Sur being on an external drive (or vice versa) and how that would work but your question doesn't even hint at that.
In the body of your question, you ask about the issues surrounding having multiple operating systems within the same APFS container; however, it doesn't support the supposition of the title - internal versus external drives. The questions, however, are valid in their own right.
You also ask if issues that aren't technically bona fide issues are resolved in an OS that's still in developer beta stats.
So as to your questions:
Is this messiness still present in Big Sur/Catalina running side by side? Does using a separate container help this?
Probably. This is still two operating systems running side by side in a single container (if this is how you choose to configure it). But, remember, this is a developer beta not a public beta meaning there are still very significant changes to come. Unless you're planning on submitting feedback to Apple trying to solve this at this stage is an exercise in futility.
If installed on an external disk, does this issue still persist?
Yes. If the issue exists on an internal disk, why wouldn't it continue to exist on an external one? Again, were looking at this from the initial position of internal versus external disks.
However, there is part of your question that could shed some light on what I assume you're asking:
Does using a separate container help this?
There's nothing that says you can't have multiple APFS containers on a single computer. You could have two internal disks, or two external disks or an internal and an external both with their own APFS formatted containers, one with Catalina (internal) and the other with Big Sur (external). In fact, if you wanted to test Big Sur, I would highly suggest you format and install Big Sur on an external drive and leave your internal drive alone. Either installation with not interfere with the other's Recovery, System, Preboot, etc. partitions.
Having multiple OSes on the same drive is obviously doable as per the links you provided, but it introduces an extra level of complexity you likely don't want to deal with. I'm all for users trying things out and testing, but not at the sake of risking data - especially if this is your "production" or "work" machine. So, yes, having this in a separate container on a separate disk "solves" this.
Ideally, you test on a computer you don't mind getting "hosed up" because you mis-configured drives, but I realize having multiple Macs is outside the budget for a lot of folks; I still encourage testing and experimentation but on a separate drive. Spending $100USD on a quality external USB drive is a lot cheaper than trying to recover your data because you experimented on your internal drive you use everyday. And, as always, make copious backups.