I think it uses the target settings for that, not the project settings. i.e. they are two seperate sets of version numbers that seem to be independent.
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Thanks so much for your detailed response. I wondered whether it was supposed to inherit, but couldn't get that to work. (I wasn't advanced enough to understand the "levels" setting or to look at that). It turns out the Apple build template overrode the default and the way to reset a default is to highlight the row and hit delete. (Don't try leaving it blank, or setting it back how you found it after the build template set it)
Next task is explore your build configuration advice.