cant comment specifically on felines but i and my mum are intolerant to numerous things. my intolerances have changed over time- huge list as a child (at one point there were about 20 things i could eat safely and nowt else) then much better as i approached puberty (predicted by dietician) and am annoyingly slowly picking them up again so i think its certainly possible he could have grown into an intolerance.
i also find with mine that certain combinations or volumes are triggers- im intolerant to wheat but currently mild so im advised to have a little day as if i cut it out my body will essentially forget how to handle it but if i have wheat cereal and sandwich for lunch ill be very ill but one of other is just uncomfortable. i cant keep down whole eggs (even just a little) but egg containing things are largely fine
so in short it sounds like it could be to me. with an intolerance the body has differing strengths of reaction, so a desert spoon might be acceptable (dilute enough) or might give so mild a reaction its unnoticeable but 2 tips the body into an over reaction.
also remember that whatever it is his body is reacting to could build up day to day so it might be a case of something is fine every other day.
My mums intolerances progressed to the point it triggered IBS and she had to basically stop eating as he system refused to keep in anything so it could be that while he was so chronically ill its damaged his stomach lining or gut lining and hes oversensitive- Neko has this problem currently, totally fine on the tesco nature turkey trays, bit of anything else and things get softer. he is now coping with a good few forkfuls of bozita and some applaws dry without any real issues and there is definite imrovement but his problems were parasitic so Riley might improve more and more given enough time?