Sorry, still don't completely understand. OR, maybe there is a different place to look for what you are looking for.
Let me start with an example, in my tree, that may get at what you are trying to say.
I am the Home Person in my Tree. I don't have a large tree, but about 8,060 individuals. I have that many, as I have done research back to the Ancestor that came to the US in about 1674. He is my 6th Great-Grandfather.
So, if I were to do a Chart or Report from the Home Person (me), looking at a Kinship Report, Ancestors of the Home Person, I would see around 526 individuals. In a Chart, there would be fewer.
I am guessing, that what you are calling a "sub tree" is the difference between the 8,060 and 526. But that's looking are the Home Person (me).
But, IF I change the Home Person to my 6th Great-Grandfather, I would get a different picture. The way the family grew over time, I have continued to research Each of the Branches of the children of this person, some "branches" down to today.
Looking at the Kinship Report again, with the new Home Person, the number goes from 526 to 2,165. That number is still not close to the 8,060 individuals in the file.
The difference between 8.060 and 2,165 is that I have many NON-Directly line individuals from either of the Home Persons.
Bottom line here is, that Depending on who the Home Person is, or Where you Start a Chart or Report, there will be many people that are in "sub-trees".
Not yet sure what the Issue is that we are trying to resolve, there is a bigger view of your Family File inthe Extended Family Chart. That CAN, if you do the settings correctly show everyone in your file. It will show, what I would call a "sub-tree". In this case, a "sub-tree" would be islands of families or individuals, where there may not be (or may not yet be) a link between these "islands" and the main tree.
Lets say I have a Family Group that only has parents and children, but haven't found "how they fit in", (the island), I could select one of those individuals, to do research to see if or how they do fit in.
So, my question is, What is the problem we are trying to resolve? Or, what is the "Main Tree"? Are you just researching Direct Blood Line members of that "Home Person"? But, what happens when you change the Home Person? That sets up a Different Direct Blood line.
Can you be a little more specific as to what you looking for? As you can see, I have many, many individuals in my file that are NOT in my "main tree". That is, when I have myself as the Home Person. Moving that Home Person to my 6th Great-Grandfather, changes that number of something less.
Are you looking for where or who to search for?
I think that there may be Charts or Reports that will help you.
Sorry if I am not seeing the problem we are trying to solve.