The others have said it all really - the penthouse is a useless piece of plastic! As are the external tubes. Might be ok in a playpen as a toy
What you've suggested doing sounds absolutely fine - remove it and the tubes while your hammy is out of the cage and pop the new house in. I would suggest keeping some of the old nest from the penthouse and putting that inside the new house - if it's pee soaked just try and salvage a bit of dry nest even if it's a bit whiffy. And put a new big pile of toilet paper strips somewhere in the cage (not actually in the house) so your hammy can forage for it, pouch it and take it back to build up the nest again. Ideally the house should be open underneath and sat on top of the substrate with at least 4" depth of substrate (they like to bury hoards under their nest).
My tip would be to get a largeish house and put the litter tray inside it - this has always worked for me - it happened by accident when I gave our last hamster a large flat roofed house to double up as a shelf and he moved his pee corner inside the house - so I moved the potty in there. Have done that since and they do seem to like having a toilet area inside the house.
A shoebox house can be good for that - cut the base out of the shoebox and keep the lid as a lift off roof and cut a hole for a door (door at one end of the long side is good as they tend to pee near the door at the back - which is where I used to put the potty - and nest at the end furthest away from the door where it's darker). Then you can just lift the lid to remove the potty/litter tray to empty it - every 5 days or so.
Alternatively just a decent sized house and put the litter tray somewhere in the cage - in one of the corners - but you may have to move it as they only use it if you put it where they've chosen to have a toilet - it's usually a corner of the cage when you have a standard sized house.
Rodipet also make good houses but they're not cheap. I have the labyrinth house for our syrian (and he does use his potty inside it although recently I had to move the potty when he started hoarding in it). But that is too large for the hamster heaven (had that size of cage previously) as it takes up too much floorspace. Coco has the two roomed granite top house which is good and about the size of a shoebox I think
Yes your hammy may have a hissy fit for a week or so after the change - on the other hand if they really like the new arrangement the hissy fit may only last one evening! And they do like a nice big house that's dark inside so they can build a really big cosy nest, hoard their food under it and snack in bed - and then go for a pee without having to come out of the house - ensuite bathroom. A flat roofed house also makes another level to put a food bowl on eg. If you put a bendy bridge over the entrance of the house it will tempt your hammy inside it because it makes it nice and dark inside - and this also makes a ramp up to the roof.
If you can do all this without moving/changing much else in the cage it will be less stressful as well - eg leaving the wheel where it is if you can and most of the toys although you may have to move one or two things to fit the house in probably.
I would also suggest only keeping one shelf (the solid one) to make room for the house and wheel. Or if you have a large-ish flat roofed house you can do without both shelves as the roof doubles up as a shelf. Rat sputniks also work well in that cage as they hang quite low and can be climbed into from floor level - they also give a bit of overhead cover so they don't feel too exposed if you remove the shelves.
For a good basic house, the Ferplast sin guinea pig house is very good - it's not big enough to fit a litter tray inside but a nice size for a nest (far too small for a guinea pig). It fits together like a jigsaw and has no nails or glue plus the roof lifts off. It would need a bendy bridge over the door really though because the door is quite large as intended for a guinea pig. It is also quite tall for that reason so best sat on the base of the cage rather than on the substrate - with some substrate inside instead and substrate around the outside. If it sits on top of the substrate it could squash a hamster if they tried to tunnel under it.
However it doesn't seem to be available anywhere any more - can only find the huge rabbit house or the tiny hamster version of the sin (far too small).
If you want to make the changes now then maybe go for a shoebox house if you have a cardboard shoe box around! Otherwise I would wait until you have the house as once they move they don't like further change. If it's a smooth wood house it's a good idea to paint it with plastikote paint which is petsafe and water based - costs about £4 for a little pot and you just paint it on with a paintbrush - it dries quite quickly. This makes the wood wipe clean and prevents staining if they do have an accident in house.
They are very funny when they move into a new house - I've always found they spend the first night making a real racket inside it - no idea what they do - scratching the walls and banging around!
These are some of the rodipet houses. You can use google translate to read things! The house Coco has is the second one down. The piece of granite is very good as it helps keep their nails short - it's rough granite. I don't have the granite topped house but have the separate piece of granite at the bottom of that link which I have on a shelf under the water bottle so it roughens their nails when they go for a drink - or you can put the food bowl on it for the same reason. The postage is about £8 though.
https://www.rodipet.de/shop/haeuser/rodipet-granit/