I can't seem to export any of the obsidian generated by making steam in a heat exchanger. Is this possible or do I have to manually go and press the Clear Buffers every few minutes?

Unless I'm missing something....if I am, sorry.

Are you using an item output port ?

Try putting a chest directly next to it or connect it to either BC pipes, TE ducts or EIO conduits.

The mod pack I'm playing (FTB Horizons Daybreaker) has none of those things. Putting a chest directly in front of the output port did work however.

So my next question would be, is the mekanism transport pipe supposed to work, or is it not supported?

Not supported for now. I'll look into adding it, leaving this issue open as a reminder :P

That was one of the things I tried. I added an Item Output port, and connected a mekanism logistical transporter pipe between it and a chest.

Nothing happened.