Looking into your service in particular, whilst it's true that it isn't a "bare-bones" run like some trains are (without any allowances for anything), I think the timetable balances performance vs time in a reasonable fashion. The exact timetabled breakdown is available
here (archived for posterity).
There's only one station stop which has more time in there than would be strictly necessary - and that's Bradford Interchange, where the train reverses. All other station stops are tight affairs, especially considering that, for example, Manchester Victoria will presumably involve a full crew change? (there may be another en-route)
So then there's just the other three types of allowances - engineering, pathing and performance.
The first is a necessity in any timetable, because on a route as long as Leeds to Chester there will almost always be a couple of temporary speed restrictions (TSRs - especially in warm weather like today) meaning that the train can't achieve the run as quickly as in perfect conditions.
There are 5 minutes of engineering allowance throughout the run - to be honest, that's probably a bit more than will be necessary to allow for TSRs on a run of that length on most days. I would have thought 2 or 3 minutes would suffice, but then again I'm not a timetable planner!
The last type of allowance, performance, is also necessary on most runs that don't run along entirely flat terrain. The kind of train used on the run can be quite variable, and Leeds to Chester involves some fairly decent ascents between Bradford and Manchester!
If, for example, a 75mph Pacer or a Sprinter (153/155) finds its way into the mix then this could hinder adherance to the timetable quite a lot, given the run is based on the train running with a 90mph Class 158 Super Sprinter. Given this, I'm surprised to see there's no allowance at all on this run - presumably this is made up somewhat by the slightly excessive engineering allowance.
So then to come to the most controversial type of allowance - pathing. This is the truest kind of 'slack' in a timetable. But again, it's a necessity on today's congested railway network. There are 12 minutes of pathing time on this particular run. To be honest, again that's on the high side of what I'd expect to see on a run of this length, but there are several points at which the train goes through veritable bottlenecks, such as at Manchester Victoria.
The difficulty is that if one particular station stop takes longer than usual, e.g. because there's more passengers than usual or there's a wheelchair bound passenger who needs the ramp taking out, then this could mean a lot of trains get held up and people start missing connections, and it all goes to pot! Unfortunately this is an area that can only be solved by planning the timetable carefully and reducing the number of conflicting movements, e.g. by adding flyovers. Unfortunately the former often means that you have unattractive journey times or irregular service patterns, and the latter is ruinously expensive.
So overall it's clear there's no easy solution to it all. Yes, you could just schedule everything with a timetable that is based on the quickest possible run in perfect conditions, but then this would mean that a lot of people would become delayed very easily, and a lot of official connections would become unreliable. Not to mention the effect on the oft-quoted timeliness statistics. So I think there's certainly a balance to be struck. I agree that on this particular run the amount of allowances in the timetable is a bit excessive, but if it means that you can actually rely on it arriving at each station when they say it will, I'm happy with that, really.