It turns out that a couple of list members discussed this a few years
ago - unknown to me yesterday, when I went through the Fitzwilliam and
Ladye Nevell versions (both Dover editions reedited by Winogron). The
result of the comparison is interesting: Fitzwilliam wins on almost
all substantive musical counts, except the single obviously
mistranscribed chord just before the last entry (c-e-g semibreve,
where LNB has G-d-g). The Fitzwilliam book also has the numbers for
the entries of the cantus firmus, which probably helped in preserving
the structure of the piece. (This may apply also to numbered variation
pieces in FVB.)

The fantasia appears on p.68-76 of the LNB edition (neither has bar
numbers) and I will go through the main differences based on that.

p.68, last bar (full cadence onto G following entry '2'): LNB has b-d'
in RH, FVB has the obviously correct a-d'.

Neither copyist or editor seems to have noticed the stretto entry of
the c.f. starting on tenor F, just before entry '5' (p.69, last
system). On the descent this turns into a syncopated stretto (p.70,
first system). This suggests that the A's in the alto should be tied
(p.70, b.2-3) though this happens in neither source.

p.70 system 2 bar 1 (beginning of entry '6'): LNB has a LH which fails
to be 3-part counterpoint and has a rather awkward bare tritone on the
last minim. FWB has correct 3-part counterpoint with the lowest 2
parts continuing in thirds (A-c, Bb-d minims, G-Bb semibreve) and the
suspended f resolving clearly on the last minim.

p.70 system 3 bar 2 (last note of entry '6', f' over a fifth d-a): LNB
has a minim rest in the alto while FWB has a crotchet e' tied over
resolving to a crotchet d.

p.70 last system b.3 (descending c''-b' of entry '7'): LNB has a chord
e-g-e' in the middle of the bar, FVB has e-b-e'. Here Ladye Nevell may
be preferable to avoid parallel 8ves between RH and LH.

p.71 system 3 first bar: an alto f' in LNB was editorially corrected
to a' to make up a chord of A major.

p.73 last system first bar: LNB has a rest in RH, c-e in LH to start
the bar. FWB has a semibreve g here and the number 13, marking the
13th entry of the c.f.. This means that the copyist of LNB actually
omitted the first note of the c.f.! Unlucky for some.

p.74 system 4 bar 3 (descending f#'-e' of entry '14'): in the bass
part LNB has two crotchets B, c then d minim tied to a crotchet. This
breaks the prevailing triplet rhythm for no apparent reason and
confuses the harmony in the second half of the bar. FWB has three
triplet crotchets B, c, d then d minim, then rest. This is
rhythmically somewhat better and allows the tenor to take over the
lowest part cleanly at the change of harmony. However, the tie between
the d's in LNB suggests an even better version: use the triplet bass
rhythm but tie the d's over the beat, avoiding the awkward repetition
in FVB.
Then the mistake in LNB is a rather crass one (wrong rhythm and wrong
harmony) compared to that in FWB (omission of a tie).

p.75 last system last bar (ascending e' of entry '16'): an alto g' in
LNB had to be corrected to e' in order to complete the hexachord.
Another place where the LNB copyist ignored the structure.

p.76 first system bar 4: LNB has, in the LH, 12 quavers f e d c d e f
g a b c' a. This is unusually bad counterpoint: e' against f on a
strong beat in a running bass context. FVB has f e c d e f g a b c'
quavers then crotchet a, which is a lot more consonant with the RH,
and melodically and rhythmically more varied.

p.76 system 4 bar 2 (ascending e' of entry '17'): the e' is indicated
only by a direct in LNB, and is absent from FWB. Score half a point to
Ladye Nevell.

p.76 system 4 bar 3 (just before descending e' of entry '17): in the
alto LNB has a minim rest, then c' minim and e' semibreve. This
creates an empty octave with the bass on the 2nd minim beat and fudges
the re-entry of the c.f. as if it were a continuation of some other
line. FWB has a crotchet rest, then minim c', then the part descends
into the LH with the crotchet g tied over the beat. (The LH a at the
beginning of the bar is only a minim.) This is better in three
respects: the middle part is now syncopated w.r.t. the bass which
avoids the empty octave; this same part now audibly moves down into
the tenor, leaving the re-entry of the c.f. in the clear; and it
introduces the countersubject which the soprano imitates a semibreve
later.

This and the comparison of 'The Hunt(e)s up(p)' indicate to me that
the LNB copyist, while he may have been diligent, did not have a great
understanding of the musical forms he was dealing with: at least he
did not use such an understanding to correct obvious structural
mistakes. The mistakes of FWB on the contrary look more like simple
sloppiness: omission or wrong placement isolated notes / ties /
accidentals.
~~~T~~~