Tycho is never POM-first, i.e. it never generates a Bundle manifests. It does however read and write the Manifest source file during the build (in order to replace the .qualifier
literal), so the manifest in the build result may be formatted differently to the original. It is however equivalent to the source.
Note that the by definition of the manifest file format, the last line of a manifest is ignored if it is not terminated by a newline character. So if this is the case in your sources, it may seem that Tycho removes a header from the manifest. This is kind of true, but only because the header was invalid and would be ignored by an OSGi runtime anyway.
AFAIK, the most recent Tycho version prints a warning if the last line of the source manifest isn't properly terminated.