I won't go (far… sigh!) into my opinions on Parelli, except to say that while I reckon most of the *principles* behind the practices are generally sound, it’s people's application, understanding and skill with those principles - be that The Man himself or otherwise, that often leaves a lot to be desired IMO. Most of those principles are actually sound behavioural ‘law’ and techniques… with Parelli’s spin on them. So while I too dislike the ‘cult’ hype and disagree(a little or thoroughly) with many specifics(as I do of most good teachers anyway), I think there is a lot of good stuff there too. Not that PNH is by any means the only source of good behavioural principles either and it sounds like you have very valid reasons for wanting to avoid it. But IME your example about Parelli horses you’ve met having no manners or not being taught ‘no’ is the fault of the handler, not the techniques or principles. Anyway, enough said on that.
What has been suggested above is mainly what can be called behaviourally as 'flooding' - the stimulus is applied & continued, regardless of effect, until the animal ceases to react. Basically, behaviour/attitude that ‘works’ for an animal will become stronger and behaviour that doesn’t work will become weaker, so in the case of desensitising the horse, reactivity doesn’t work – the ‘pressure’ doesn’t cease, but accepting it does – the handler removes the stimulus. I think it’s a sound tactic of itself *for many situations & horses*. It is indeed one of the techniques that Parelli, among many others use, and at a guess, I’d say that may be what he was attempting in the example you gave. It is also the principle in play when ‘breakers’ of old would just get on a horse & ‘ride out the bucks’ for eg.
But IMO what can be wrong with doing this only, without consideration for what else is going on, is that while depending on the horse & situation, “Eventually he'll come to the realisation that he won't be hurt by you.” this could mean a whole lot of stress, even to the point of mental ‘shut down’ in the meantime. Also mental shut down may cause a horse to appear to accept the procedure without actually becoming desensitised/confident of it, so may mean chronic continual stress. Then you might have a horse that is ‘obedient’ but ‘suddenly, for no reason… etc’ drops his bundle, or a horse that you’ve got to keep repeating the procedure if the horse has been given time off to regain his ‘spirits’ …”My horse can’t be left unworked or he goes feral”
Even when ‘flooding’ eventually gets positive results, horses learn by association and repetition and the more ‘practice’ the animal has at whatever attitude/behaviour, the stronger it becomes. So if the horse is subjected to scary stimulus, his attitudes about being frightened by someone will often get stronger too.
Know of the ‘left brain right brain’ theory? It is said that the left brain controls the thinking side and the right controls the emotional, instinctive, automatic side. Also that it can be difficult for a horse to actually think at all when a situation causes it to ‘go right brained’. I think that it’s important to avoid the horse switching to his right brain if at all possible.
So while the basic flooding principles are still important, I use ‘approach & retreat’ tactics to get there, so I can gradually get the horse confident with stuff without pushing him too far past his comfort zone. Start wherever the horse is at in the situation & be prepared to progress at whatever pace he can go, where he’s perhaps on guard but still thinking. I will repeat the stimulus at that ‘level’ repeatedly(but in short ‘sessions’, with stress free breaks) until the horse is truly confident & blasé about it before gradually asking him to accept a little more. In that way, you retain his trust & confidence(strengthening his positive attitude about you generally) but push his ‘comfort zone’ gradually towards the goal.
If/when you get to a point that’s too much for him, there’s no harm in backing off – you’ve built a strong foundation & you only need to step back to show him you respect him & mean no harm & then you just continue at that level before again progressing further, perhaps a little slower or more gradually. *This method can well be as tedious as it may sound to begin with, depending on horse & situation, but if you aim to start slow & consider the horse’s attitude and avoid sending him ‘right brained’ there is no confrontation or force so the horse tends to quickly ‘get it’ and progress can then be rapid. (This also happens to be a technique Parelli advises BTW)
With your horse & his previous(& early – double ouch!) bad handling, I would expect it will indeed start slow & take a while to get him solid. It sounds like you’ve already been doing well with him, but you don’t say how long you’ve had him/worked with him? If it’s a short time, I’d also just continue your other training with him and develop a really solid relationship & training there first. Then just start wherever he’s at, be that picking up a roller when you’re still 10 metres away or standing beside him & raising your arm as if to put it over him.
I would also be incredibly careful of who you choose to start him under saddle if you’re not doing it yourself, because quite aside from the safety factor, any too pushy/hurried tactics could bring the old fears flooding back(pardon the pun). Also horses don’t generalise well, so if you’re the only good handler he’s known, he’s likely to be skeptical at best of a stranger before they even start.