You want to get myco actually on your roots in most cases, it takes a long time to establish itself in your soil and it requires a root to be present to even start the process, also if they touch your root if there are any endophytic fungal strains they could possibly migrate into the root for safety.
I haven't popped a seed in years but I usually dust my roots every time coming out of the cloner. I would assume you would want to dust the taproot or put myco in the hole directly along with the seed while sowing, not sure if either would be better than the other, but you would especially want an auto flower to be exposed to myco as early as possible. Mostly just because an auto will likely spend less time in the soil than a photo plant.