I hated teleporters and spinners in dungeon crawlers (ugly memories of Bard's Tale 3 on the c64), unless there was a good auto-mapping system.
I know there's been games where I was trying to manually map but gave up because of devices in the dungeon that displace you, be they teleporters, trapdoors, pit traps, spinners, and so on. There's a number of things to consider when thinking about this, most of which rely on realism versus suspension of disbelief. For example, if I'm making an auto-map, do I just assume that the player knows the dimensions of the dungeon? Are each of the floors directly below the one above it? Are the floors all the same size? How would the player know any of this? One of the problems with developing something like this is deciding how much will the player even think about versus how much will you think about this developing it. Also, if the player does think of these things, will they even care? Of course, you can always give the player a device from the start to explain the auto-map such as a magical or technological device that creates a map if you're worried about such things.
But I agree with you, displacement in the map can be fun and interesting for the player, but a way to re-orient themselves is a good idea. The challenge can be that the map shows where they are, but there will be a gap in it so they'll need to find their way to connect back to the known corners of the map should they intentionally or unintentionally get displaced.
Should I have a noob zone to level up? Because level 1 is a bit weak.
This is a tough call. There's reasons to do it, but there's also the case for getting right in to the action. One solution is to make level 1 not as weak. Another solution is to start the character at a slightly higher level, which you could possibly do as part of character generation like the background stuff in Mount & Blade. I always thought it was kind of odd that in Mount & Blade, you could spend your teenage years training as a solider, but still be level 1. You could always set the purpose of the player being on the ship to suggest that the character had a little background in minor adventuring, because it would be odd for a baker or tailor to get shipwrecked and then decide to adventure through a tower dungeon right afterwards.
You could also have the catacombs connect to the tower dungeon, making the catacombs the "newbie" dungeon but only recently became an issue because they were expanding and breached the tower which started waking up the dead in there. So, you start off in the catacombs with lower level things like skeletons and extremely withered zombies and the worse things be in the actual first floor of the tower. This could even grant the player the choice of going straight to the first floor of the tower, which will be harder but more reward, or they could start with the easier catacombs to gain some experience and better starting loot.
Either way, don't let the faggots discourage you. Make the best possible game you can make right now, and learn from it. Don't get overly ambitious, but also make the tools you could reuse later on.