@Twigg Many questions indeed, I will try to answer them as accurately as I can, so if anyone knows more, feel free to correct me.
Before answering your questions, I think it is necessary to clear any misconceptions about the Android kernel.
Most Android devices don't support mainline Linux, so the upstream kernel can't work on the device, as it is missing specific drivers and device trees. That is because the SoC manufacturers (Qualcomm/MediaTek) use an older kernel as a base to test their new designs, and that old kernel is subsequently used by the device manufacturers (e.g. Fairphone). Of course, neither of them bother isolating the changes to create a pull request to upstream Linux (due to costs etc.). As a result, Ubuntu Touch developers have to do extra patches to make the downstream patched kernel work for them.
Does you mean that the FF5 did not support mainline Linux?
Yes, Fairphone officially didn't, but the community has (see the PostmarketOS port)
Why the change with FF6?
I don't know. Maybe they hope they can attract more Linux enthusiast (like us).
I wonder about the advantages/disadvantages to using mainline Linux vs the Hallum approach
Mainline Linux enables more flexibility and a desktop-like experience. However, it is more difficult to make everything work there, postmarketOS is a great example, as almost none of their devices currently support the same hardware features as they did on Android. Not even Qualcomm themselves have succeeded in fully working mainline Linux kernel, as the recent Snapdragon X Elite chips which were made to compete with x86 still don't have full Linux support.
Halium on the other hand uses the same downstream kernel as Android does, with some adaptations for Ubuntu. It also runs the Android drivers on an LXC container, which allows easier access to hardware. As you can imagine, this has limitations, as we can't change the Android drivers and pulling patches from upstream Linux can break functionality.
I presume that this amounts to a desktop equivilence to doing a clean install of Ubuntu, vs installing it in Windows?
I don't get your analogy. It would be more accurate to say that to install normal Ubuntu, you have to reverse engineer the Windows drivers. However, in Ubuntu Touch's case we can reuse the Android drivers as the Linux kernel remains mostly the same.
From what I have read above, it looks like there haven't been too many changes from FF5 to FF6, so perhaps that makes it easier for Ubuntu Touch to get released on the FF6?
Each device needs its own port, sometimes even devices with the same chip require very different ports. In this case FP6 seems vastly different hardware-wise than FP5 so I don't think they would be similar software-wise.