You can find the second and later versions in sys.numbered_procedures.
Wouldn't this behavior depend on which version on Management Studio you're using, rather than the SQL Server where the procs are deployed? The Object Browser SMO libraries are defined in the client, not on the server.
I tried this on SQL 2008 R2, SQL 2012, and SQL 2016 (both as client tool versions and as target server), plus the latest SSMS 17.9.1, and in all cases the Modify option scripted both versions.
I found this link saying Modify does not script both versions in SQL 2012 https://stackoverflow.com/questions/12546418/modifying-numbered-procedures-in-management-studio-2012 but I could not reproduce it. Possibly it was fixed?