IFT, the following is just supposition on my part.
Rolls Royce recognised the importance of utilising the jet thrust available from the exhaust as a means of increasing performance. Broadly speaking, the exhaust thrust contributed some 10% of the engines output (have figures of test carried out by Hawker on a Hurricane Mk II with a Merlin XX at various altitudes).
During the Spitfire trials a number of different exhaust set ups were tried - stub, streamlined, ejector, streamlined ejector and ducted ejector. The ejector types were trialled with five different sized nozzles, with 3" being considered the best all round. The prototype Spitfire was able to increase its full power speed at 20,000 feet from 334 mph with stub exhausts to 347 mph with the ejector type.
The first Spitfire to have the individual stacks was the Mk VII, and this came about with the first use of a two speed, two stage supercharged Merlin 61. (NB - I should add that experiments with exhaust configurations seem to be many. A Mk VI was fitted with individual stacks experimentally to reduce glare during night flying, as was a totally enclosed system). The Merlin 61 was designed to be a high altitude engine, with a full throttle height in FS gear of 23,500 feet, nigh double that of previous versions. I'm guessing that the individual stubs on the 61 were optimised for some particular sweet spot, the previous ejector in use would not have been optimised for the higher gas flow emanating from the exhaust.