I think there might be some confusion about pinching out... the advice has always been, for tomatoes which produce fruits of a medium or large size, stop them by pinching out once 6-8 trusses have formed, and that means all over. It is not necessary to do this at all with smaller tomatoes, such as cherry tomato varieties.
UPDATE: I made a comment below, but decided to add it to the answer with more detail - as I said, if you're growing a cordon variety, these are grown as a single stem, tied to a support, and only 4 trusses are allowed to develop. Side shoots are removed to keep the upright shape and limit the number of trusses. Examples of cordon tomatoes are Ailsa Craig, Alicante, Craigella, tumbler, Moneymaker - there are many more, so it rather depends on the variety you're growing as to how you treat them. Note that four trusses is usual in cooler climes with a shorter growing season - hotter parts of the world tend to restrict to around 6. The other group of bush varieties need no such treatment, though some of them may need staking (such as Pixie).
Note that cotyledon refers to seed leaves rather than lateral (side) shoots; laterals may also arise from existing branches, at the ends. All should be removed so that you just have leaves which arise from the main stem - beyond 4 (or whatever is appropriate for where you are) trusses, you 'stop' by taking the top off. Later in the growing season, towards the end, as ripening goes on, if there are a lot of leaves on the main stem, many can be removed to enable less shading of the fruits.