Ok major news. I believe I've figured out how to reliably get the x-t1 and shutter release working while tethered to the pi. It requires following a specific sequence of steps in order to work.
1st: Boot up the pi and camera and connect the relevant cables (shutter release + micro usb)
2nd: Launch kstars and ekos
3rd: run the capture module with a simple imaging sequence. I usually do between 2-3s exposures with a count of 2 or 3.
4th: You will notice as the exposures begin, on the camera LCD the exposure time indicator will change from BULB to 30s. Anytime exposure starts using the shutter release and the camera shows 30s exposure will fail. Let the first exposure run and fail, and on the 2nd, shut off the camera and then turn it back on. The time will revert to bulb and it will start taking bulb exposures not tethered to the pi. It will save these junk exposures to the SD card.
5th: This is very important. Either wait for the imaging sequence to abort, or cancel it yourself. Then click on the first 'tab' ekos starts at and click disconnect. Once disconnected then click the red telephone button. Then close the ekos window through the top right x, and then do the same for kstars.
6th: Relaunch kstars and ekos as before and begin an imaging sequence. You will notice this time the camera LCD will not change from BULB to 30s but will stay at BULB when taking exposures.
These exposures will be saved to the pi and will not be saved to the SD card. You can now begin imaging as normal.
I have no idea what exactly is causing this behaviour, but it seems to be something to do with the tethering. I have a suspicion that the X-T1 does not support bulb exposures when tethered, and can only do T-mode exposures (up to 30s). However by doing the steps above I think it might be altering something to do with the tether to allow changing of settings and downloading of exposures while still getting bulb to work. I am not technically inclined enough to know as to how to begin investigating this behavior. Perhaps someone with more knowledge could do so.
In a couple days I will have clear skies and will test my entire setup. If everything goes smoothly, I will write up a complete post as to how to get the fuji x-t1 to work with astrophotography. There are many more issues I have ran into besides this that I think others would be greatly appreciative to know how to solve. Here's to hoping everything works!