I had forgotten about that conversation. Sorry!
Testing a little more here with my modifications, I checked that the alternate recipes are hidden on the player crafting menu, on machines, on logistics requests. I only see it cluttering on the Factory Search!
Then I added this line:
item.flags = create_alternate_items and {} or { "hidden" }
And appears to solve the problem.
Currently, I prefer this behavior (could mine my custom spidertron and build it again, without loosing the configuration!)
Thanks.