That's a very good point. I guess the difference is that at Borough, there's only one flat junction to the west - between the fast and suburban lines to Charing Cross, whereas to the West of Castlefield, you've got lots of them.
One flat junction in a busy area is relatively easy to deal with by timetabling, as long as performance is good so trains mostly arrive at exactly the expected time. Trains on the same route in opposite directions can then be timed to pass each other on the junction. If there are multiple flat junctions in quick succession that trick usually can't be pulled more than once and capacity has to reduce. This is one reason capacity at Castlefield can never approach that of Charing Cross or Thameslink, where a similar situation applies with the one flat junction south of Blackfriars.
The length of the double track at Borough Market doesn't really affect the capacity much, as long as it has no stations on it. Having two useable platforms in each direction at Piccadilly and Oxford Road would means that trains could use them alternately, so platform dwell and reoccupation times would probably no longer be the limiting factor in capacity (and if they still are they would be much less severe). Deansgate is still a problem as it only has one platform in each direction, so any train stopping there takes two paths, but I suspect clever timetabling may allow those gaps to coincide with gaps that are needed anyway to fit the flat junctions.
I don't believe four-tracking the corridor would help much, as the platform dwell and reoccupation times would constrain the frequency on each track so the total capacity wouldn't be much more than achievable by sorting out the two stations as previously planned. The extra tracks would have to continue to somewhere around Mayfield loop so some trains on the northern tracks could cross over onto other tracks before reaching the merge, otherwise the bottleneck east of Piccadilly would be just as bad as Castlefield Junction is now. As mentioned above, unless train routeings were simplified to an arrangement more like that of London Bridge, the number of crossing moves would probably kill any capacity benefit of continuous four-tracking.
If there is money to sort out this corridor then I suggest the first priority would be those platforms and the next would be to grade-separate Castlefield Junction, as this is where trains split out from the busy corridor so is probably most critical. There may just be space to build a flyover for the Up line from Cornbrook to rise up to the same level as Metrolink, pass right over the junction and merge back in the vicinity of an abolished Deansgate station. If this isn't possible then grade-separating Ordsall Lane would provide some degree of relief. But it would need some detailed simulation modelling to quantify the capacity and performance benefits.