If the idea is from Varisys and they should have known that you need certain software and drivers for it that are closed source they should have had a plan how to support it in future. If not why integrating it? And why integrating it in X5000 yet again?
The idea obviously came from Varisys, no "If" about it. Yes, they should have thought more about the difficulties in porting the control software, or development tools, and maybe they mentioned it, or maybe they did not think of that problem at that time. I don't think Varisys guys had any experience or knowledge about AmigaOS4.x or the capabilities of the Hyperion developers working on the port. It appears that the XMOS chips had peaked the interest of at least one or more people high up at Varisys, which is why they made the suggestion to integrate one of the chips onto the Nemo motherboard, without regard on how the tools would be ported to AmigaOS4.x.
Varisys was only concerned with the hardware side, and it was A-Eon's and Hyperion's responsibility to port AmigaOS4.x to the new hardware and write all needed drivers. Varisys only made sure the hardware would run Linux, so they could test all hardware on the motherboard and get A-Eon to "sign off" on it being finished and working. They had no responsibility or concern on how any of the hardware would be supported in the future by A-Eon, or Hyperion.
As for your question on why it was integrated onto the X1000 motherboard, I think that answer has already been explained a few times. It was an inexpensive way to make the X1000 motherboard different or unique, and provided a "user-definable" chip and interface to Amiga users. Something to make it special, even though some people choose to criticize the decision and usefulness of Xena/Xorro, it does not change the reason(s) for initially adding it to the X1000 motherboard.
Only Trevor and Matthew can answer why it is still being added to their next AmigaOne X5000 motherboards, but I would guess that they still believe that the Xena/Xorro combination will be utilized in some interesting and productive way in the future, either by some 3rd party developer, or perhaps A-Eon has an idea of their own for some use or product that will use the Xena/Xorro interface. I perceive the availability of Xena/Xorro on the X1000 and X5000 motherboards as an opportunity for owners of such systems to be creative and develop any kind of software and hardware projects that they can imagine. If removing it from the X5000 only changes the price by $20 or $50, or even $100, then it makes more sense to me to keep it.
It does not matter how much a few people protest, or campaign against the usefulness of Xena/Xorro, specially when those few people are not X1000 customers. Those opinions are not going to change the decisions of Trevor, or Matthew, though I am sure that both of them are well aware of the valid arguments for and against continuing to include Xena/Xorro on their future motherboards. The development cost on how to add Xena/Xorro to a motherboard has already been paid out on the X1000 design and development costs, so adding it again to the X5000 does not include the development cost, only the cost of components. Perhaps Trevor has a good deal with XMOS on the price of the Xena chip, who knows? I would guess that compared to the over all cost of the X5000 motherboard, the addition of the XMOS chip to it is very small and removing it would not change the price of selling the X5000 motherboards or complete systems very much, so any small cost savings are probably not enough incentive to Trevor and Matthew to give up on Xena/Xorro yet.
There are always going to be a few people who have different opinions and suggestions on how to do things differently, specially in this community, where there are so many different choices to continue the spirit of the Amiga. There is no way to please everyone, all of the time. It will be interesting to me when someone finally does utilize Xena/Xorro in an interesting and productive way. What will all the people who say Xena/Xorro is completely useless say then? It reminds me of the few who were so sure that the Minimig was a hoax and could never be accomplished. But I am also open minded and realize that it may take years for anything interesting to be developed for Xena/Xorro, or that maybe it will never happen. And if nothing ever becomes available for the Xena/Xorro combination, I won't blame Trevor and the Varisys designers for trying to make something unique available to the end users. Some attempts at innovation work and some don't. Maybe it will turn out to be a bad idea, but I don't believe that we have given it enough time to make that determination yet.