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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.
Thanks a lot for your response, I didn't get a notification.
Yes, my aim is to find differences between pathogenic and nonpathogenic bacterial strains. So in this case I think it is ok as it can consider them as different species.