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Time spent under a category D national visa does not count toward the 90 days period for short stays in the Schengen area, the rules are clear about that. See Getting a tourist Schengen visa after working visa and Does tourist visa (90 days) apply after a long-term visa ends in Schengen countries?
One issue is that if the course was under 90 days, it would be perfectly fine to follow it without a visa, which would in turn force your partner to use her 90 days for the course (that's probably the reason behind the minimum duration for student visas in Spain). But if she gets a student visa for a course lasting longer than 90 days, it has to be a category D visa and time spent in Spain under this visa will not count towards the 90-day limit for visa-free short stays in the Schengen area.
Provided the Spanish authorities do grant her a visa, you could even theoretically stay 9 months in the Schengen area (3 months before the start of the long-stay visa, 3+ months on the long-stay visa and 3 months afterwards).