Sabrina
Welcome to the forum and thanks for the first Post - hopefully many more in the future!
I am not sure what you mean by you are unable to have an opening where the trenches meet? However I am guessing here and will try to answer the question
1) Each pipe run is separated out and has its own Trench definition. The original requirement for the Utility Module was for estimating purposes not specifically for building trenches for machine control etc. however of course people want to use it for that also. So the trench sides are not looking for a connection to a side run which is why they are "solid where the two trenches meet.
2) You can use the linework generated for the trenches to build a composite trench system, editing the lines to get the intersection areas as you need them and then use that edited linework to build your composite trench model. This also is how you solve for crossovers in the trench surfaces that can sometimes occur at tight angle corners etc.
If you need help with that please let me know and I will record you a video on how to edit trench linework to make a combined surface model.
Alan