Yes, it is a bit difficult to understand the implications. You can use all kinds of roll paper with the iPF5100, it is just that the Media Type you select is limited in some cases. This isn't a practical problem with matte papers, and wouldn't be a problem if you got a custom profile made with a compatible Media Type. The place you would run into trouble is if you had a generic profile made for one Media Type (Photo Paper Plus Semi-Gloss in the example) that could use sheet paper, but not rolls. The profile wouldn't work with your roll paper. The roll paper itself could be used, but you would have to get a custom profile made for it (or find a generic profile made for that Media Type).
The problem isn't that bad, and certainly not a reason to avoid getting the iPF5100, it is just a shame that Canon is hobbling the software in this way and causing extra problems for users. This is the opposite of the HP approach, which is very much an open system re: Paper Types set in the software.
However, don't take this as a recommendation for the HP--it has its own set of problems, including star wheel marks on glossy papers for some and reports of problems with getting good reds on some matte papers.
From what I know (and I haven't worked with the HP), I would still recommend the Canon. Of course, HP also doesn't make a 17 inch printer, which makes that decision easier
--John
