That has always been one of the main differences between TS and JTV recordings, because the JTV file set must be in a unique location, or at least be uniquely named. It would get very messy to have multiple JTV recordings accumulating in one directory. With TS format recordings it isn't so bad, but it could still create a directory with lots of files in it.
You can get what you want with TS recordings and existing functionality though. Just add custom tagging to the recording rules that you are using, to update the [filename (path)] tag, and MC will save the recording to the directory defined by the tag.
For example, I have most of my Series recordings now setting the [filename (path)] tag to "E:\Recorded TV\[Series]\Season [Season]\" so that each recording is in a directory specifically for the Series and Season it belongs to. In my case, because I use JTV format recordings, I get one more sub-directory below that, which then contains the JTV file set.
If you wanted each Episode recording for a Series in its own sub-directory by itself, which might be a bit of overkill, you could set the [filename (path)] tag to "E:\Recorded TV\[Series]\Season [Season]\[Name]\".
Or for non-series recordings, just set the [filename (path)] tag to "E:\Recorded TV\[Name]\", or perhaps "E:\Recorded TV\[Name] - [Date Recorded]\". You get the idea.
There is even a setting to apply default tags when a recording is done at "Options > Television > Recording > Recording default - Tags to apply when recording is done", which you could set to, for example, "E:\Recorded TV\[Series]\Season [Season]\". But that would have mixed results when a recording isn't an Episode of a Series. In that case, the directory created would look something like "E:\Recorded TV\Unknown Series\Season Unknown Season\". But setting a default would add the tag to a new Recording Rule created, which could then be edited as required. Sort of like a template. There is also a right-click function in the tag value edit box, which allows you to select recent values, add fields, and so on.
Note the "\" at the end of the examples above. That is required and important.
Does the above meet your needs?
You will find more information if you search the Television forum for [filename (path)]. There have been a few discussions.