I may be lucky in having medium length, broad-ish fingers on a broad-ish palm, which probably makes these things easier for me than for some folk… FWIW, then, I use top-joint pads on L hand, kinda modified flute position with no tube contact lower on L1 as on flute - it is quite comfy and relaxed and no strain ensues. My R hand goes to a kind of semi-pipers’ position, not because I can’t span/seal the tone-holes with the end pads (I can, no problem - see pic below), but for a more comfortable wrist angle at that arm-extension from the body, which necessitates a cocked wrist (thumb-side of hand tipped upwards) if you try to use a hold that brings the fingers in with their long axes roughly perpendicular to the long axis of the tube (as on flute R hand). I put R3 end-pad on hole, R1 middle of 2nd pad on hole and R2 as it falls naturally between those anchor points, just below the crease of the upper joint on the outer part of the 2nd pad, which brings the fingers to the tube at nearer 45 degrees and straightens the R wrist… I find this perfectly natural and switch between standard “Rockstro” type hold on flute, standard all upper pads on high whistles and this compromise/mixed posture on low whistles…
You can see my “semi-pipers’” position (as just described) in exaggerated circumstances on this video clip I did for another thread on a low Bb tube or on low D whistle on YouTube.
NB, I do not have massive hands (thumb-tip to little finger-tip full spread = 9"/23cm, palm width at base of fingers = 3.75"/9.5cm) though they are quite flexible.
OK, afterthought: here are some pics on this I used to have up in an old thread, but they were on a now-defunct hosting account so have disappeared (or I’d just have linked the old thread!) - so I’ve loaded 'em up again:
Low D from front, “semi-pipers’” (R1&2 maybe a bit less laterally advanced than I described above):

Low D with an all-finger-tip-pads only hold - note awkward angle of R wrist compared to 1st pic above, though spanning the holes is no problem:

And my “semi-pipers’” hold applied to a low Bb tube with offset & raised 3rd finger holes - I probably advance R1&2 a bit more now than when I took this picture as I have lately noticed strain in my R wrist more and to relieve that straighten it by tipping the near side of the hand towards the tube, which pushes those fingers forward/across the tube more, pivoting on R3’s pad on its tone-hole:

Just for comparison, my normal hold on a high whistle from front and side angles:



Note: thumb positions make quite a difference too - experiment with moving your thumbs around, both up/down tube and laterally around it, watching how the changes affect your hand posture, until you find an optimum compromise for comfortable hand/wrist angle and finger-approach to tube and secure support of the whistle.
Also, I think that if you advance all 3 R hand fingers to use the 2nd knuckle-pad on the tone-holes, that actually reduces your available span and re-twists the wrist - try making small adjustments and watching/analysing their postural/mechanical effects.
(Edited to make a small additional note and expand some of the original comment/description…)