If you do an online A-Level course you will receive the same qualification from an exam board as someone studying at an in-person college. You will still have to sit the exam in person and will have to travel to an examination center (such as a local college) and pay for exam fees if not provided by the online college.
I personally haven't done an A-Level online but there shouldn't be any major disadvantages in the study material. You won't be able to seek advice face-to-face from your teacher/tutor but if you are motivated and able to be responsible for your studying, you should do fine.
The best thing to do would ask those two online colleges as they will be able to answer your questions and future queries.