These are good points. I think thumbless has a lot of gappy chords because most chords are gappy, and thumbless uses a lot of chords. There are two reasons for this. 1) by adding Shift and Control to the chord space, thumbless has to squeeze the whole alphabet into the first three fingers. 2) the coding for which thumbless is designed contains a lot of punctuation, and some of it uses up fast chords because it is more frequent than a-z. Assuming you are not writing code, only (1) is a useful tradeoff for you.
I'd like to agree with your assessment about fast transition between diagonal chords, but I think there's no doubt that gaps (diagonals) slow chords. Here are some statistics from Twidlit (Tutor > Compare Button Times) for my chording times. Here gaps are calculated as the sum of the positional distance divided by the finger gap for each pair of adjacent fingers (examples are shown).
Gaps in chord: 0 0 0 0 0 0 1 1 1 1 1 1
1/6 2/6 3/6 4/6 5/6 1/6 2/6 3/6 4/6 5/6
Example chord: '|'| -||' -|'| ,||' -'|| '-|'
Chords: 45 0 4 16 2 0 56 0 0 12 0 0
Mean (msec): 848 0 1087 1151 1082 0 1204 0 0 1599 0 0
Gaps in chord: 2 2 2 2 2 2 3 3 3 3 3 3
1/6 2/6 3/6 4/6 5/6 1/6 2/6 3/6 4/6 5/6
Example chord: ,'|| -|,' -,'|
Chords: 58 0 0 4 0 0 32 0 0 0 0 0
Mean (msec): 1453 0 0 1716 0 0 1762 0 0 0 0 0
Gaps in chord: 4 4 4 4 4 4 5 5 5 5 5 5
1/6 2/6 3/6 4/6 5/6 1/6 2/6 3/6 4/6 5/6
Example chord: ','| -','
Chords: 20 0 0 0 0 0 4 0 0 0 0 0
Mean (msec): 1877 0 0 0 0 0 2255 0 0 0 0 0
Gaps in chord: 6
Example chord: ,','
Chords: 2
Mean (msec): 2443
If you are writing predominantly the alphabet, you are missing out on high speed low finger count and inline chords assigned to other keystrokes.
Be aware that if you replace CtrlShift with GUI much of the power of cursor word-based selection will be lost.
I'm really pleased you are finding some benefit in thumbless. My recommendation would be to adapt it to lower the priority of punctuation in favor of the alphabet. Twidlit would help.