For the most part, in Europe Marquis is considered a higher title than Count, but it is the other way around in ACKS.
I believe historically this is because domains near the frontier (marche / marca / march) came with greater military responsibility, and hence prestige. I could see the argument for it being the other way around in ACKS because of the benefits afforded to building a domain in a civilised area, as opposed to a borderland or wilderness one, but I still find it a bit strange.
I think one could argue that in order for a domain to be able to expand enough it needs to be on the border in the first place, with baronies and counties inside the civilised area but relatively small, and marches either close to the frontier but with a civilised core, or formerly on the frontier, now big and fully civilised, and retaining the prestige they acquired through war.
Perhaps it would depend on whether civilisation as a whole is on the decline. If it’s doing reasonably well, domains on the border would be in demand from more ambitious and talented individuals. During periods of contraction, it would be the other way around.
Technically, the default setting doesn’t even use those titles — it uses Castellans, Tribunes, Legates, Palatines, Prefects, Exarchs, and Tarkauns. So it’s perfecly simple to switch around or even replace the “common” types completely. As for myself, I would generally replace Marquises with Viscounts and Princes with either Peers or Grandees, depending on whether the setting is Low or High Middle Age (if it’s Late Antiquity, I’d use more Romanesque or Hellenistic names).
That being said, even though I would have generally preferred Marquises to be above Counts, I don’t think that switching those titles around would do anything except cause confusion if someone tries to use 1e books with the II changed titles. So you should do it, but I don’t think it should be in the book.