I will tentatively say yes, but it depends on what are your research questions. You can simply concatenate proteome files if there are no name clashes. It may emit a warning about duplicated sequences, but I believe you can just ignore this and move on.

However, phylogenetic inferences among species may be affected by doing this. Otherwise, the only other consequence I can think of is the reference/centroid sequence used to assign orthogroups may change.

An alternative to concatenating files is supplying a proteome for each isolate/strain/etc... that you are using and it will treat it as a different species.