That gunk is break material, proteins, and hopscum, and it is in all brewing, even extract. The "loss" is simply how much from your final boil volume and then your settling in long primary or secondary you "lose" before bottling or kegging.
I varies from recipe to recipe, and depends on your grains, adjuncts and hops in your recipe.
Some dump everything in, without straining, just pour it in the bucket or in the funnel....Some use a big strainer that fit in the funnel for a carboy, or a sanitized 5 gallon nylon paint strainer bag in the bucket...
I have done it all ways. It really doesn't matter...anything will settle.
In other words, there is no wrong way to do it, or better way, or way that will make the best beer...they all work...the choice is what will work the best for you. That's how you develop you own unique brewing process. By trying all ways and deciding what works best for you.
What I do with my IC, is chill the wort, then I lean the bottom of my autosiphon about two coils up from the bottom on the metal of the siphon. That rests it above most of the break material and trub, then I rack it to the fermenter until I'm down to that and carefully lower the siphon down into the gunk, just trying to get as much of the wort as possible without letting in the hops and break matter.
But pretty much up until I got my immersion chiller for christmas last year I just dumped for the majority of my batches.
So just leave it, it will all settle out in the fermenter.
Everything's fine. some folks over compensate by making their recipes 5.5 gallons instead of 5 figuring about a half gallon due to trub loss. I don't bother and I still usually end up with 5 gallons. I find that a long primary compacts the trub and leaves me more beer.
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