On a large worm, after inserting the hook through the nose and turning it around, I push the hook almost all the way through but just before the point protrudes. On a fluke, I push the hook completely through and skin hook it on top. I've tried both ways on a baby brush hog (3/0 round bend hook), but am not sure which way is better. Any suggestions?

Baby Brush Hogs are a very small diameter thickness. You can skin hook it if you like. I do not and have not missed much on hook ups with that size hook. It rips through the plastic easily.

Depends on the bait for me. Leaving the hook inside the bait is definitely more weedless, but with some baits I feel I miss fish that way. Just have to experiment and see which works best for you and which way you have confidence in. I would try it skin hooked first, and if you find yourself getting hung up then bring the hook back inside the bait.

I just wanna be able to feel the sharp tip without it sticking out. Just almost out. Fluke you need wide gap and then come back and skin hook it. But after a little use or catching fish my flukes starting getting worn and I just keep using with hook completely exposed. Until I have to change that is.

Worms and brush hawks skin hooked fluke exposed.

I Texpose (skin hook) all my plastics no matter what they are for a Tx.rig, both weighted and unweighted, drop shot, and a Carolina rig. I use Owner rigging hooks in 1/0-4/0 depending on what bait I am throwing and I also like Owner J hooks in 2/0-5/0 again depending on what plastic I am throwing. I quit using round bend hooks many years ago because (for me at least) it is harder for me to skin hook a plastic and have it hang straight with an offset round bend hook. I have no problem with the rigging hook or the J hook.

A 2/0 or 3/0 rigging hook works great on a Tx. rigged baby brush hog and on a Carolina rig I use the 1/0 rigging hook for my drop shot finesse worm.
I use the J (wide gap hooks) for flukes and larger baits.

I push my hooks through then pull them back inside just to where you can't feel the point of the hook.

I use a 2/0 hook for all my TX rigged plastics. I'll even throw a 4" worm using that hook.

I use 3/0 Gamakatsu EWG for almost all my soft plastics. 7" power worms, chigger craws, lizards, brush hogs.... I use a 4/0 EWG Superline Gama's for most weightless plastics like Flukes, Rattlesnakes, LFT Ring-Frys(my favorite weightless)...because it gives me a near perfect weight/fall for "weightless" plastics. I will go up to 5/0 EWG Gama's for larger plastics like 10"-12" Powerworms, Zoom Ol' Monsters... But back to your question: on smaller plastics without much body/meat like the Baby Brush Hog, Bubble Fry.... I use the 2/0 EWG light wire Gama's and in every case I bring my hook through the body of the bait and "skin hook" the point back into the top of the bait. I do believe though if you were to leave the hook point set in the body with these thinner bodied baits without bringing the point thru I don't think you would have a bad hookup rate because the hook will come out of these easy.