Thank you for your reply.

So does that mean, it impacts only the behavior of the "juncCounts" (-J) parameter and not at all the counting on meta-feature (i.e. gene) level or anything else? If so, to how many junctions is featureCounts limited in normal (i.e. short read) mode and how many are supported when setting the "isLongRead" (-L) parameter? I tried to find this in the user's guide but couldn't find any information on it.