He be coming home late is a dialectical phrasing that means, as you surmise, he [habitually] comes home late. It is associated especially with African-American English and Caribbean English.
Linguists call this the invariant be or habitual be. Be is not simply a replacement for is; he be coming home late means he customarily or regularly comes home late, and not that he is currently in the process of coming home late. Some discussion of this in layman's terms can be found in the Slate article Why We Be Loving the “Habitual Be” by Katy Waldman, at the Lexicon Valley blog.
The meaning of lyrics is highly subject to interpretation. As Mark Foster is not a native speaker of African-American English (so far as I know), the lyric may be intended to paint a certain image of the narrator or setting, but it might simply have been an artistic choice for sonorous qualities aside from any cultural connotations. It's also impossible to know whether he is aware of the natural use of the habitual be or, as many do, he thinks he can drop it in anywhere to replace is, or if "Robert" thinks so.
Using dialects of minority communities is always fraught for an outsider, so I would advise the average English learner to stick with more standard English (e.g. he "always" comes home late).