Can I have a list of the pipes that i can use to run items in and out of the compact machine? I would like to use the buildcraft pipes, but they pop items out of the compact machine and seem to not be compatible.

Everything that is using Forge Capabilities is compatible.
Sorry, there is no good possibility to create a list of supported mods unless done manually.
But item routing in particular is often fixable by adding in a buffer chest/hopper at one side of the tunnels.