"Come on Up to the House" is a gospel song in Tom Waits' idiosyncratic style. It's sung as a direct address to some unnamed person, presumably each of us as individual listeners. We're never exactly sure whose perspective Waits is singing from when he makes repeated entreaties to "come on up to the house." It's possible that the "house" is Heaven itself... or maybe just Waits' house.
One of the song's most mysterious lines, "The world is not my home, I'm just a-passing through" is taken from a Jim Reeves song that uses that line as its title. Reeves' song opens with the lines:
This world is not my home, I'm just a-passin' through
My treasures are laid up somewhere beyond the blue
The angels beckon me from heaven's open door
And I can't feel at home in this world anymore
Waits' use of Reeves' song suggests the theme is similar. This is Waits talking to someone about the hardships of life and offering them someplace or something better. Waits doesn't deal with overtly religious themes often. Another song on Mule Variations, "Chocolate Jesus," even seems to make fun of Christianity or, at least, have fun with it.
Still, it's hard to listen to "Come On Up To The House" as anything but a sincere expression of faith to someone lost in the mist of futility.
The line, "Does life seem nasty, brutish, and short" is a reference to philosopher Thomas Hobbes and his book Leviathan. Hobbes contended that democracy was dangerous because people are essentially selfish and self-interested, meaning that allowing common people to vote for leaders would thrust mankind into civil strife, "war of every man against every man," leading to life being "solitary, poor, nasty, brutish, and short."
Hobbes believed rule by king was the best of all for the reasons above. It's hard to imagine Waits agrees with that concept, judging by the everyman nature of his songs and his antiauthoritarian ideals.
A variation in the line, "whipped by the forces that are inside of you" was used in Waits' song "Spidey's Wild Ride," released on Orphans, Bawlers & Bastards in 2006. That album compiled outtakes recorded from 1984 to 2005, so it's possible the song was written and/or recorded before "Come on Up to the House."
The same line also came up in a 2002 Austin Chronicle interview. The interviewer, Margaret Moser, asked over the phone where Waits was as they spoke. He responded, "I'm out on my own recognizance in the day room, gluing pieces of macaroni on cardboard and painting it gold. After that I get to make a belt that says, 'Whipped by the forces within me' on the back."