The MRC's eligibility criteria can be found in the MRC Studentship Handbook. They clearly state that a 2ii + a relevant MSc is acceptable. It may be that the institutions you are applying to only take 2i's - they are perfectly at liberty to do this, but should not be misleading you about MRC policy. The same applies to most other UK funding and you should not let the funding body put you off applying. You could always email the supervisor before applying to ask if they will consider your qualifications. The British Heart Foundation is an independent charity and only accepts a 2i or above.
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