Hi, zen1. I seriously doubt your ds has strong muscles all over (how can he, if he isn't exercising them climbing stairs, etc????), so the neuro describing your ds as having strong muscles is unhelpful, except to the extent that in the very general sense it means he is highly unlikely to have a neuromuscular disorder (ie a problem with the muscles themselves).
When ds1 saw a neuromuscular specialist (not the same thing as a neurologist, but someone who has more detailed understanding of the muscles themselves...) and the specialist physio she worked with, they tested the muscles around his hips, knees, elbows, shoulders, neck, etc, and there were very specific areas of weakness in an otherwise normal profile which, rather unsurprisingly, coincided with the areas of greatest hypermobility. The weakness followed a pattern they had seen before in children subsequently diagnosed with extreme hypermobility. Basically, you may have perfectly normal muscles, but they are certainly not going to develop into normally strong muscles if you aren't able to use them because your joints are too loose for you to get the stability to exercise them in the first place (and maybe your proprioception is such that you don't get good feedback as to whether or not your attempts are really working, making it hard to gather the will to perservere without a bit of assistance) - and hoping normal daily activity will cure the problem is a bit of an optimistic hope if your child cannot indulge in "normal" activities, yet... You need someone to make more effort to work out which muscles are being used inefficiently or not at all and which ones are being overused so that proper help can be given to strengthen up the muscles that need strengthening and teach your ds to use his body in an appropriate way and not in a way that is inefficient, ineffective and harmful in the long term.
My ds1 used to stand (holding on) with his knees bent backwards if you put him in a standing position - basically he was locking them back the wrong way because he didn't have the stability around his joints to maintain a standing position any other way (or, probably, the proprioceptive awareness of what his knees were doing....), and the result was he was then immobile standing up - he couldn't even sit down, because his knees were stuck... and even once he was walking, for the first year or so he would adopt a funny stiff-legged gait, particularly when going uphill, as the only method he could apply to the task when not all of his leg muscles were sufficiently developed to walk more normally. Until the muscles around his hips were a bit stronger, he also had a tendency to fall over sideways, which is not exactly normal in most children...
As for getting your ds into a crawling position - I guess he's getting quite old for this, now, but since I had to start out teaching our ds1 at 15 months old how to roll over and get himself to sitting, and his head lag meant he had to do this from his tummy (too hard to sit up from lying on his back and too hard for him to do this from his side at first), I was taught to put him between my open legs once I'd rolled him onto his tummy and basically teach him how to push himself backwards with his hands so that his knees bent underneath him and he ended up in a sitting position on his knees and then spread his legs out in front of him into his favoured sitting position. Sitting behind him with legs open stopped his legs just slipping backwards when he used his hands, because he'd back into me, until he'd worked out how to help his legs fold up in that position. From this kneeling position, with hands in front of him, we started, when he was about 17 months, lifting his body and bottom up to put him in the crawling position and encouraging him to put weight on his hands and would literally move his hands and feet in the crawling pattern, whilst basically supporting his weight and doing most of the work for him... it didn't take him long to start trying to do it himself - normal muscles do build up quite quickly if they are being used appropriately and the child concerned is confident that they can do the manouevres being asked of them!
As for pulling to stand - his weak, pronating ankles meant that he didn't really start progressing with this until he had piedro boots, which stopped his feet going out in a Chaplinesque sort of way. Once he did have boots it was again a case of getting him into kneeling, holding on to a table of appropriate height, then getting one foot out from under him and planting it solidly on the floor at the correct angle for pulling up and then physically shifting his weight onto that leg and hip so that he could pull up on it and bring his other leg up and onto the floor in a standing position. We also physically manouevered him to learn how to cruise along the furniture, because this strengthens the sides of the hips (by putting hands on sides of hips and sort of lifting them up and sideways to give him the idea of the action....). So I guess we really did teach him to go through all the stages other children go through in learning to roll over, get to sitting, crawl, pull to stand, cruise and walk, because each stage helped develop slightly different muscles.
Ds1 is now 7.5 and he really is very active and able to join in with all the things his friends do, but he wouldn't be in that position if it hadn't been for quite intensive help early on to get him moving and, in the last year, quite a lot more intensive help (or not so much help as commitment on his part to doing exercises every night which, when I tried to do them, I realised were actually extremely hard work!!!!!!!) to get specific muscles stronger, so that he stopped complaining about his legs hurting when he walked, etc. The good thing now, though, is that he does seem to have evened out his muscle strength sufficiently that he can just be active like a normal boy and maintain most of the benefits all the hard work has given him - because there is absolutely no way he would want to have to keep doing all the exercises he was given every day in the last year all his life!!!!!!!!!
Sorry about the extended essay!!!!!!!