Don Pedro K was a first hand witness in my incredibly last minute application to apply to university. Due to unforseen circumstances, I applied as an individual rather than through my school meaning that I could choose my reference (my private a-level biology tutor). The UCAS process at my school was complicated and slow and doing it by myself within three days was far easier. If the relationship with your referee is good then go for it! To make my reference stronger, I sent supporting references from a pharmacist and GP that I have worked with. Get someone to check your personal statement too which Don Predro K did for me which was very kind and helpful! Always good to have another opinion.
In my case, applying without the school was better. If I did it through them, I would have been predicted lower grades, a referee from someone that didn't teach me my subjects and so doesn't know me that well, and limited into what universities I could apply for. I couldn't be happier with an offer from Newcastle and UEA for biomedical sciences with the option to transfer to medicine. Good luck! and thank you Don Pedro K. o K.