Hi there
You're thinking on the right lines. It does take them a couple of weeks to settle in and it sounds like he is a shy nervous type anyway.
So I had something similar - you can't get them out if they're hidden under bedding! I would definitely go ahead and reduce the amount of bedding until he is tame. It is what I had to do. A good option is to give them areally good house in the detolf, that mimics an underground burrow, then they tend to move in. I have a labyrinth house for our hamster and that works every time, but any large house will do. Large enough to build a big cosy nest and to fit a litter tray inside (because when they have a large house they tend to move their pee corner inside the house too). Basically it allows them normal behaviours so they can nest, hoard and pee in chambers of a "burrow".
A shoe box house is fine. Cut the base out of the shoe box, a hole for a door on one of the long sides (near one end is best ratherthan in the middle as then it's darker at the other end). And use the lid as a lift off roof. I am sure you'll have space in the detolf for one. Then put a smelly treat inside (eg cucumber or cheese) and he will probably move into the house within a couple of days. It can really help if you put a bendy bridge tunnel over the entrance too - the tunnel tempts them to go in the house and it makes the house darker inside. Put a corner litter tray in the back corner opposite the door with chinchilla sand in. Any dish will do but corner litter trays fit easily and stop splashes at the back.
So - then you know where he is! And can tempt him out of the house with a tube over the door with a smelly treat at the far end. He will walk into the tube, then you can put both hands over the ends and lift him out in the tube. It's easier if you have a hamster ball as you can then put one end of the tube in the hamster ball, keep the other end covered and he'll walk into the ball. Then pop the lid on and you can carry him in the ball to a safe place to let him out for some taming and interaction (eg the dry bathtub). Just put the ball down in the bath, take the lid off and he'll walk out. Having the odd toy or tunnel in the bathtub helps.
Timing:
Most people find it is best to get them in a routine of being woken up at feeding time - eg around 6pm. They will then get in the habit of knowing it's feeding time around then and start waking up for the food. Make a bit of noise putting the food out - a bit of slight clanging etc so it wakes him up.
Our last syrian was very shy and lazy and would never come out voluntarily - I always had to tempt him into a tube - and he was fully hand tame.
So substrate - yes reduce it so he isn't hiding away. Maybe 5" deep. With the house, you can have it sitting on about 2 to 3" of substrate and pile the other coupleof inches round the outsideof it - so it's part underground. You can channel out/scoop out a bit of substrate near the entrance.
Then try and do feeding time at the same time every night. And at that time, tempt him into a tube and have him out for some hand taming. A playpen area is also a good area for taming as you can sit in it as well and they run over you and get used to your presence and scent.
He is coming out late to avoid everyone! They do vary but I found activity varied at different times of night. eg 6pm our hammy was incredibly active and fast. 8pm was his naptime and he was easier to handle and more interested in going to sleep under a blanket than making a run for it. 10pm onwards they are very active and a bit harder to tame as in "night mode". But whatever time is best for you putting food out. I find the earlier the better seems to work - our hammies seemed to be waiting for it from 5pm onwards. Our Syrian then wants to sort his food and go back to his house and is more interested in coming out around 7pm to 8pm (when he's in that mood!).
It doesn't matter if he's super active at the time you get him out, let him burn off some energy and take the taming slowly, with the occasional stroke while he's out.