I am not convinced; are you absolutely sure it's nothing to do with the fact that the connections in question are within the same company?
Certain. Again as I said above (I think I edited after you quoted) in specific examples it might be feasible (with constraints) but often it simply will not be.
In any case, this isn't a satisfactory situation; if what you say is true, then there is still a root cause that shouldn't exist.
The root cause is late running and the aim - as I said - is for incidents to a) reduce in number, b) have less impact when they do occur. This is reliant on Network Rail (who are 'responsible' for the majority of incidents) and TOCs having a focus on this, although of course this is much easier said than done and we can point to a host of reasons why trains are delayed. Perhaps some timetable optimisation at certain hotspots to improve connectional times, but again train planning is incredibly complicated and reliant on so many factors to get right. Something that seems simple could get a 5 minute explanation from a planner on why they would love to do something but why conflicts / other trains / timetable rules prevent it. Or doing that would impact something else down the line which now wouldn't align.
But ultimately if trains are running late, something has to give.