Auscitrus rootstock seed info..
"seed is heat treated at 52 degrees C for 10 minutes and surface sterilised with chlorine before being dried
then treated with Thiram fungicide for cool storage"
As far as I know, Thiram is applied for seed storage and germination protection.
Alternaria is listed as one of the pathogens it is used against.
https://www.cropscience.bayer.us/seedgrowth/thiram/pestThiram is not used on all Fungi / pathogen problems. Pythium doesn't seem to be listed ??
Similarly other Fungicides would not be effective against Alternaria.
Good hygiene is also important in seed collection, such as picking fruit before it falls to ground, extracting seed before fruit goes off.
Cleaning seed thoroughly of juice and pulp etc, using new zip bags for seed, sterilising tools and strainers with boiling water between seed types/lots.
Working in a clean area, i.e. kitchen when wife not home !!!
Cleaning your hands between seed lots.
Cleaning/sterilizing the the peel of any older, fallen, mouldy fruit etc before getting to the seeds.
Soilless propagation mixes should reduce pathogens, as should heat treating the mix components ( usually not with fertiliser added ).
Heat could be steam, boiling, solarisation.