simple logical conclusion, wood filler is NOT a solid, rather a viscous putty (wood putty as it is also known) and is designed to be COSMETIC rather than structural.
as in an earlier illustration, to increase the ability of a semi-rigid fibrous material to bend (EX: wood), one can:
Allow the outer area of the bend to stretch, (heat, moisten) to increase malleability/elastic properties...
OR remove material on the inner surface to DECREASE the compression of material (making area with decreased material thinner) therefore to MAINTAIN the rigidity of the structure (IE:the fretboard laminate of the neck)
replace the material removed (the fret, made of METAL) with something with nearly the compression resistant properties of at least the surrounding material (wood) would be preferred.
will it work with PUTTY!!!???
YES.
Will there be issues and lost stability in the structure?
YES!!!
With the putty be more susceptible to environmental issues besides squirting out as the neck flexes due to mechanical changes, and it's less than perfect adhesion to the slots and oily wood.
Ya fer sher yu becha!
Has it been done 10000 times with few reported issues YEP!
is it worth all the effort? NO
a fretless neck from EBAY would be a better solution.
to OP thanks you for the detailed post your methods look to be well considered, and are sufficiently sound for most intents and purposes.... just not sound "best practice"
a good if not BETTER solution would be a strong 2 part epoxy filling the gaps, being fluid nearly ALL of the gap, assuming air bubbles do not form, and surface tension will allow ingress sufficiently via capillary action (harder than the wood without the "sawdust" component to weaken the structure) colorant would not be necessary but could be kind of cool and while at all this effort float the entire surface with epoxy

.....
or buy an ebay neck for 100.00 (i repeat myself)