With people wanting to become a Clinical Scientist, there's always a misunderstanding in regards to where they stand in the laboratory.
Traditionally, you would have Band 2 support staff and then Band 5-6 scientists, with a Band 7-8b management team. You would then have the Consultants (Consultant Microbiologist, for example), who deal with the clinical interpretation of results and liaise with wards, inform them when an urgent result has occurred etc. These are qualified doctors who have gone through the ranks and specialised.
You asked what the difference is between a MLA and an AP. I think that should be obvious given an MLA is Band 2 and an AP is Band 4. Traditionally, there was quite a gap between the MLA support staff and the scientists. It meant the scientists were doing some jobs that were not quite as skilled as they should be doing, which is financially inefficient. Band 4 AP's were brought in to take some of that work off them.
So where do Clinical Scientist's fall into this? In a similar way to AP's. They bridge a gap between the scientists in the laboratory and the Consultant's. There is however, an issue here. Clinical Scientists have been abundantly taken on within areas such as Biochemistry and Haematology. Their use instead of Consultants is widespread. That is, however, not the case in Microbiology. Clinical Scientists exist, but very sparsely. I'd say roughly, each of the largest labs in a region have one. Leeds, Sheffield, Manchester have a single one, and they're often quite R&D based.
The reason for this is in Microbiology we are still trained to be able to interpret results, and so a lot of results are actually authorised by the scientists, unlike in Blood Sciences where the scientists are loading the samples onto the analysers and the vast majority of results are automatically authorised based on validation rules.