On Tue, Jun 21, 2016 at 12:54:48PM +0200, Jakub Jelinek wrote:
> Right now the St. Gall neumes above staff are emitted using the same
> infrastructure as <alt>...</alt>, so for the spacing in between the base
> line of the neumes and the staff or between the top of them and previous
> staff/line of text applies whatever can be used for <alt>.

That said, for production I'm still using gregorio 4.1.*, and the base line
of the neumes I think has been in constant distance from the top staff line,
rather than variable depending on the height of the notes.
If that is something that changed in 4.2, it would be indeed very much
undesirable; I usually try to roughly use the semi-diastematic heights from
the Mss, but just manually increase height or move neumes horizontally (left
or right) if there are too high gabc notes, so that it doesn't clash.
I'll need to try your source tonight on both gregorio 4.1.x and 4.2-rc*.
If it indeed changed, it would be nice if that behavior is used just for
<alt> text and not for nabc above line neumes.

Looking at your sources, tad is invalid syntax, did you mean tahd or just
ta?  Other than that, I bet the tractulis belong on usQUE and morTEM
syllables, rather than the preceeding one, and
http://e-codices.unifr.ch/en/csg/0359/96/0/Sequence-499
agrees with that and I feel the mellismas on auTEM and cruCIS are too long
so it is better to align more precisely the Cantatorium neumes on the
quadrata.  So (untested) something like:

        Jakub
name:Christus factus est;
gabc-copyright: Abbazia Benedettina Mater Ecclesiæ - Isola S. Giulio (NO);
score-copyright: Abbazia Benedettina S. Maria Assunta - Praglia (PD);
office-part:Graduale;
occasion:In hebdomada sancta;
commentary:Philp 2, 8-9;
transcriber: Sr. Maria Ruth Malagoli OSB;
transcription-date: 20160614;
mode:5;
language: latin;
nabc-lines:1;
%%
(c4) Chris(ffg|vihd/pe)tus(f.|ta) *(,) fac(fg|pe)tus(f|ta) est(f|ta) pro(f|ta) 
no(ghFED.|toS2sut2|ge__|cl-hh|!/fg|peShi)bis(f.|tahe) (;) 
o(f|ta)bé(hf!/gh!jj|cllsc2//vi-hhpp2``vi-hkpohn|!/0kjl)di(jij|pf1lsc2)ens(hg__|cl-)
 (,) us(hv_!JJH|vi-/tgShj)que(f|ta) ad(ixfiHGh|///pesu2vi) 
mor(fgf___|toS)tem,(f.|ta) (;) mor(ixf!hho!i>|///ta-sa>hh)tem(g|ta) 
au(gjj|pe`vi)tem(ixjh|///cl-|iw!jvIG!/|qihhsut2|hwivHG>|ql-hhsu1sux1) 
cru(fvfsfs~_|vi-ds-)cis.(fd!/|cl-|fg!hvGF!/|vipp2sut2|egOhfhg!/|sa-hetoS2hg|hvggof.|vihg``pr)
 (::)
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