There's some good advice on this thread and some dreadful bits as well.
Fees-wise: as long as she was resident in the EU at the time of the end of the transition agreement on 31st December 2020 (which sounds like she was based on 2 years there already for IGCSEs), as a UK passport holder she is entitled to home fees under the terms of the withdrawal agreement. This stands for courses started until 2027.
Number of A levels: the school probably offers International A Levels, which still have a standalone AS. Therefore she'll probably be dropping one after a year anyway. Most international schools tend to follow that model still, so students aren't limiting options as quickly.
Language A Levels: very few universities discriminate against students taking native languages, in the same way they don't against English speakers taking English language. In many cases they can't legally, as this was challenged in the courts by a group of Urdu speakers a few years ago. It used to be the case, it now isn't. I recently asked every rep this at a large university fair, only UCL said they don't recommend it. All this is irrelevant as the UCAS form will show clearly that the student hasn't been in Spain all that long, and so Spanish isn't anywhere near native anyway.
Subject choice: more varied. If there is a chance she might change to engineering or chemistry degrees, or Nat Sci at Cambridge, then further maths would be better IF she loves maths and would do well at it. Big IF there though.
If she's sure she wants any kind of biology or biological science, then the Spanish is an equally valid choice, especially if she loves it and will do well in it.
Teacher reasons: the teacher may be trying to recruit a great student to their department as they want the numbers or want to teach her. Often students with loads of Astars at GCSE get inundated by teachers trying to convince them to take their subject, as all teachers want the great students in their class. They're looking at in isolation though, without knowing the overview of her other subjects, aims, and preferences. On the other hand, they may genuinely know from conversations from the other teachers that the Spanish will be a challenge and is trying to gently steer her away from taking it on eithout upsetting her. The fact that it's a Head of Stem rather than Head of 6th or a teacher that knows her well does seem like a flag that they might not actually know all that much about uni admissions though; they have changed a lot from when any teacher applied to uni.
Source for all of this: I'm a university advisor, I work with 120 students per year in my sixth form advising on A Level choices and uni applications. Currently further way, I previously did this job in Spain for 9 years.
Final point- the article ranking A Level subjects is bollocks. Please don't read it.