I understand you're not having a go, the problem is it's impossible to give you an answer without seeing what the actual traffic picture was and what other considerations there were.
The controller may have told you what they thought the reason was but it was actually something else - we don't always get told why the next guy won't allow something, particularly if things are busy the response will just be "not available".
In the end accuracy of position is just one consideration. There are still many aspects of ATC that rely on the controller brain rather than automation so running things along the rails allows the human brain to cope with more traffic as it reduces the processing workload. Randomly scattered tracks increases the workload as we have to manually search for the conflicts. Fine when it's quiet, not so good when you're busy.