Is Jun secretly in love with Boss man? I hope not, poor guy.

I don’t think so.
His expression when he saw Mujin and Wuyeon kissing was more surprise than hurt, and in. An earlier chapter when he was driving Mujin to the apartment building where Wuyeon lives, he asked him if he was visiting a secret wife. I didn’t get the feeling he was feeling sad/jealous (for example, I was just reading Monochrome Rumor and in a flashback scene, ML was asking MC is he planned to marry and MC was like “nah I don’t feel that way about her” and ML said something like “if you marry, you would still try your best to love her, so don’t marry”).
I think Jun just really cares for Mujin in a non-romantic way.