David,
It depends on what you are looking to do with the XER Files.
The Command line utility can only create new projects & cannot update existing projects - not sure if there is a speed advantage in using this option as the Primavera Desktop application is not open during this import process. This will require some understanding of creating batch files & modifying XML Files to enable this to work. I have only used this for file exports & not tried the import option.
I would personally not recommend going down the xerFileParserBuilder route to merge multiple xer files, unless you really know the structure of the XER files & that you confirm thtat there is no duplicate key values in all the XER files - potential to corrupt yor entire database this way. It is also likely to take you longer to do this than just importing the files normally!
Please note that while the xerFileParserBuilder can be utilised to modify xer files, it also has the potential to create errors in your database. Calendar Data can grow considerably depending on how many calendar exceptions there are in the source database - excel has a maximum size limit for the amount of data each cell can contain & there is a potential that this could be exceeded. Activity Notebooks is another area where this data cropping may occur. Not saying not to use it - just to use caution!
If you are looking to compare XER files that contain the same project to allow comparisons, then you will be best looking to import each one separately so that if required you can rename the projects on import (in my opinion anyway).
I would also suggest having different databases if possible for each client, as there is potential for global data to be changed between the different companies (easy to do if using an SQLite Database format).
Regards,
Steven