Yes, it seems to be the standard among all SkyTeam frequent flyer programs that any sector coded with a "flight" number (even if actually operated by train, or the KLM bus between Ottawa and Montréal) of the airline that operates (or, in the case of Flying Blue, participates in) your particular frequent flyer program, you get credit.

But as soon as you take a flight on an airline which is not the native airline of your chosen frequent flyer program, then the rules is that it has to be operated by (and not just coded as) a SkyTeam airline (i.e. actually on SkyTeam metal - so no trains, buses, or non-Skyteam operating airlines!!!)