Perhaps instead of a true well deck the ships could have a alcove which is permanently flooded which would "Hug" 1/3 to 1/2 of an LCM to over come this issue? This would not be the LCM permanent stowege as it would be deck stowed. Two smaller LCM's may be a better idea than one large one.
The crewing may be high and is only an estimate. However the AWD's have a crew of 184 and I wouldn't see the crewing requirement being much less. Also remember only one of the four would normally have a company of troops embarked and the other three are doing normal navy stuff, which means boardings which require a lot of man power.
I think you're trying to make it too much of a hybrid amphib/destroyer, with full capacity as both.
The F125 & Absalons, in their different ways, are compromises which make no attempt at that full capacity in either role. F125 has been described as a colonial cruiser: it's equipped for self-defense, maritime security (e.g. anti-piracy) & limited littoral intervention, with excellent endurance. Absalon is equipped for self-defence &
flexible littoral intervention, with a deck which can be used for transport, accommodation, stores, or a variable mixture. It does the same as the F125, or can function as a self-defending transport - because the Danish navy is too small for specialised ships.
Both get by with a crew of about 100. An AWD needs more because it is far more heavily armed, with more sensors, & expects to get into serious warfighting, which isn't appropriate for this ship. Is it meant to double up as an AAW destroyer? Can't be done: you won't fit the weapons & sensors in & keep the troops. Is it meant as a real landing ship, able to put men & vehicles ashore on beaches in rough seas, & thus need a dock or fancy hull? If so, then you have to give up on the idea of anything like frigate performance, & you'll have problems fitting in the weapons. Landing craft take a lot of space.
I don't agree with Abraham that the whole idea is a mistake - the colonial cruiser & self-defending transports were very successful types, as long as they stuck to what they were meant for (whether the RAN can justify 'em is a different matter, but I'm content to leave that argument to one side for the moment) - but I think you've not accepted the degree to which a compromise ship must compromise. The point of a ship like this is that it can function autonomously, or as head of a flotilla of minor vessels, in a lowish-threat environment. If it needs AWD protection (the implication of it needing AWD crewing, in a similar size ship), then you send an AWD, & in that case, it's unlikely that a company is enough, so you'll send something bigger to carry the troops.
Any crew carried for boardings & the like will not be needed when carrying troops (use the soldiers!), & their cabins will therefore be available. The F125 will have a permanent complement of 160
including 50 commandos.