Yes, it'll still take you to the following world, I dunno if there's any other hacks that do this, but NSMB5: Clone Tag Team 2 does it, in all castles (except for the first and final castles) instead of bosses, you get to rooms with enemies that you must kill in order to make a door appear that'll take you to a room with the flagpole, however, some things you must take into consideration is that the level will not end until Mario/Luigi hit a solid tile that stop them, and you'll still get to the following world even if you put a secret exit flagpole (obviously, secret exit flagpoles don't work in levels that don't have secret exits, lol)
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I'm also working on a hack in collaboration with  crook,  Rph,  Digital Cheese and  RetroAleXD. Check out this thread for updates.

A door or the destruction of tiles that previously blocked off a hallway are good too. The reason I thought of spawning a warp pipe upon killing the enemy-like boss is because of SM3DL. The Boom Boom/Pom Pom fights on the airships.I know that, yeah. In the vanilla game, there's a wall of three or four solid tiles on the right side of the end castle. Discovered that when I glitched behind the flagpole. Secret exits in castles wouldn't really be necessary if the linear world order patch (or whatever it's called) is applied, though. But nice to know that, with some effort, we might be able to make a NSMBDS hack with Koopalings someday, using a flagpole at the end instead of a key spawned by a vanilla boss.

I believe secret exit flags actually do work in the sense that the game won't crash or do something else that's strange. I think it just takes you to the next world just like the normal flag.

Ehh,  KingYoshi,  Mr. Ztardust already mentioned that secret exits in castles take you to the next world like the normal exits:Also, it would be nice if we figured out how to give courses without secret exits in the vanilla game, like W1-1, functional secret exits. I'm pretty sure the data for normal and secret exits is stored in some kind of table or something, so it should be possible to hex edit that. Correct me if I'm wrong.

regarding flagpoles in castle levels, in addition to what ztardusts already mentioned i believe if you grab the flag as mini mario youll be taken to the secret world you can do so via world map editing

So IYRC (if you recall correctly), flagpoles in castles would also work without the linear world order patch - World 4 would still be accessible without hex editing a warp cannon.So I was wrong. I thought it to be a lot more difficult.

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I'm also working on a hack in collaboration with  crook,  Rph,  Digital Cheese and  RetroAleXD. Check out this thread for updates.

Lol, you accidentally wrote your post in my quote, and my post in  Keeper's quote!

Just curious, and wanting to return the focus of this board to NSMB after the drama I caused yesterday. I apologize for that. So: I know that if you put tiles with lava behaviour and tiles with water behaviour in the same view, the water will glitch out and act like lava. But what if you have a room in a castle. In that room is a massive stretch of lava blocking your progress. There's also a ? Switch in the room. You press it. All lava tiles get removed and replaced with tiles with water behaviour. Given that the lava and water tiles aren't in the same view simultaneously except during the switch-around, would this make the water behave properly, allowing the player to swim in it to the other side instead of being instakilled? It would be a nice gimmick.

to my understanding having a lava stage object will make water tiles behave like lava, but lava tiles can coexist with water and water tiles