Re FK-9 and German registration:
At least in Germany you would need a German microlight licence (Luftsportgeräteführer or Sport Pilot Licence (SPL)) for flying any aircraft in the D-M*** range. These flying hours do not count for (e.g.) renewing a PPL, so I presume that they wouldn't count towards an ATPL either. In Germany, microlights are legally speaking not aircraft (Luftfahrzeuge), but belong to the same category as e.g. paragliders (Luftsportgeräte).
I believe, however, that the FK-9 (which is a really nice aircraft; I've flown a Mk III quite a bit) is nowadays also available with an EASA PtF and/or in the ELA-1 category (or whatever they call it this week; the precursor or temporary measure before the introduction of the EASA LSA), just like e.g. the Remos GX or Flight Design CTLS is. A PPL is required for flying such an aircraft, and the hours accrued should this count 100%.