I see no reason that it should be automatically disregarded by a university
I didn't say that it would be automatic.
However, it is hardly unheard of. A swift Google turns up:
www2.le.ac.uk/departments/medicine/applying/entry
If you are taking a language as one of your subjects we will ask for a declaration that you are not a native speaker of that language.
www.bath.ac.uk/study/ug/prospectus/subject/psychology/entry-requirements/
languages which are intended for non-native speakers are not normally acceptable when taken by native speakers of that language
www.nottingham.ac.uk/business/programmes/ug/admissions/index.aspx
We will not accept language A-levels designed for non-native speakers when taken by a native speaker.
www.city.ac.uk/mathematics-computer-science-engineering/about/faqs-informatics-undergraduate
We do not accept language A-Levels where the subject area is mother tongue. Language A-levels are designed for non-native speakers, so first language speakers will be at a strong (and we feel unfair) advantage. If the language is not your mother tongue we would need to see a letter from your school/college, before we can re-consider our decision.
These are all pretty mainstream universities.
Conversely, Durham has a blanket statement they will not apply such a policy, for any course.
www.dur.ac.uk/undergraduate/apply/faqs/?faqno=2459
Some universities (eg, Trinity College, Dublin) state that all of the exams should have been taken in one sitting.
That's common for medical schools, as well. My point is rather different, however: why would a conditional offer be given in terms of existing A2s? If you've got an acceptable A, and the requirement of the course is AAB, then your offer isn't AAB, it's AB. Similarly, a course might require specific A2s (for example, if you're applying for medicine at some med schools with A2 Maths, Physics and Chemistry you would need to have AS Biology as well) but the conditional offer will not mention the AS; you've already got it.
The OP needs to talk to the university to clarify, so that come next Thursday they know where they are.