Your case is covered in the book in this section. The idea here is that your files are no longer a wall-to-wall coverage of a territory. The LAScatalog engine is designed to process las files that encompass a territory where each files is spatially related to its neighbourhood.
In your case the files are independent. You basically want to loop through each file. In this case you can put this information in the catalog
opt_independent_files(ctg) <- TRUE
Each file will be processed independently, without buffer. This is equivalent to a regular loop (but with parallel capabilities and real time monitoring).
In addition depending of what you are doing you may want to avoid final merging
opt_merge(ctg) = FALSE