To me, the common translations of both suttas mentioned above are questionable, particularly SN 12.25. In other words, I personally see little correlation in the above question.
Regarding SN 12.25, ‘kaya’ quoted above obviously means ‘physical body’ since it is clearly distinguished from speech & mind. However, the common translation of “kāyasaṅkhāraṃ (bodily volitional formation)” is questionable since it occurs within the context of ‘kāyasañcetanāhetu’ (bodily volition). Why would the Buddha, within two paragraphs, use the different terms kāyasañcetanāhetu & kāyasaṅkhāraṃ as though they were synonymous, as seems to be translated? If ‘kāyasaṅkhāraṃ’ was intended to refer to bodily kamma, then the term ‘kamma’ should have been used. Worse is the translation of ‘sukhadukkhaṃ’, which is not generally used for ‘pleasurable’ and ‘painful’ feelings (vedana), as inferred, but as karmic ‘happiness’ & ‘suffering’ in general (i.e., the final outcome of dependent origination).
I have posted somewhere before that Step 3 of MN 118 (experiencing sabba kaya) is obviously the same scope as Step 7 (experiencing citta sankhara), just as Step 4 (calming kaya sankhara) is the same as Step 8 (calming citta sankhara). ‘Sankhara’ here cannot mean ‘formation’ (since ‘citta formation’ would fall into the 3rd tetrad). The term ‘kaya sankhara’ was probably not used in Step 3 because the practise is greater in scope than experiencing how the breath (kaya sankhara per MN 44) conditions/influences the physical body (kaya). To me, ‘sabba kaya’ means ‘all kaya’ & the practise involves experiencing the conditioning relationship between the mind (nama-kaya), breath-kaya & body (rupa-kaya). Please note the special & important sub-explanation in MN 118 about the 1st tetrad is: “I tell you monks that in & out breathing is a kaya among other kaya”. Thus ‘kaya’ here is not one thing (only the physical body), which is why the translation of ‘all kaya’ makes sense to me. Since when was “sabba” translated as “whole” (kevala) rather than “all”?
In conclusion, the word ‘kaya’ in SN 12.25 may not have the same meaning as in step 3 of MN 118. 