Yes, generally столица means Москва. But I think there may be some exceptions in some repulics like Tatarstan, Buryatiya, Saha and others. They have also their own capitals, but Moscow is the capital for the whole Russia
But Russian is not only spoken in Russia. When used in other (more-or-less) Russian-speaking countries, could this refer to other capitals? If said by an Ukrainian speaker, could this refer to Киев, by a Belarusian speaker of Минск and by an Estonian speaker to Tallinn...or does that have to be clarified in those cases.
I mean it's all context dependent, if you're in Ukraine and talking Russian and someone says they live in the capital then yeah it's going to mean Kyiv. If you're in Russia regardless of who's talking it's probably safe to assume that "stolitsa" is going to be Moscow, unless you say upfront: Я живу в Украине, в столице, then they'll understand that it's Kyiv specifically.
In translations of older books I've seen "capitals" used to refer to Moscow and St Petersburg collectively. I guess the reason was that no matter where the actual government was seated, they were so much more important than any other city in the Empire. Is this use of столицы still current at all?