Nevermind - I took a look at the code and I understand what is going now behind the scenes.
In case it is useful for others reading this in the future... the message "Registering fieldmap to structural" is generated regardless of whether you specify the "--nofmapreg" flag.... but if you specify --nofmapreg, the code skips the flirt based fmap --> T1 step and instead uses what seems to be a "dummy" transformation ($FSLDIR/etc/flirtsch/ident.mat).
Thank you
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