Many thanks Rado for verifying it's fine in practice and there's no general known issues on this problem (appreciate that there are quite a few places where CSS overriding may occur). Humble apologies for the css typos - overzealous when stripping out the test comments on editor submission.
So have tested deeper and found the problem - doh, I left a white.css from the copied App_Theme folderset and it conflicts and overrides the centering. Because it only kicks in on runtime, VS didn't show the problem when looking directly at the MasterPage, so an ASP.NET thing, not Sitefinity (the .aspx test page using the master showed fine because I'd also added the CSS manually to the Master for design-time viewing!). Sorry about that, should have dumped unneeded CSS and kept Theme folder clean - not used to using them, but know now!
For the best Master Page setup to save these kind of issues, it's naturally best to do a reality check on a page from master without any hardcoded css links, that way it will be practically the same as Sitefinity Template handling. The only way to do that is to use styleSheetTheme
not just theme
in the web.config:
| <pages theme="<theme-name>" styleSheetTheme="<theme-name>">
This may hopefully save others from my erroneous path! Cheers,