I've repeatedly tried to import a sequence of RAW files, shot in Manual exposure, with large changes in ISO and shutter speed through the duration.

When I try and add into LRT4, it won't allow me to click on the HG button.

I've tried clearing and reinitialising the metadata, to no avail.

The log file says that RAW files were shot in Auto, but when looking at the EXIF in Lightroom it clearly says they were shot in M.

You can also see by the screen shot that the changes in exposure are much too large to be confused with an Auto setting change.

LRTimelapse just evaluates Exif Data to see if it was shot in Auto or M.
But you can always set 2* and 3* keyframes manually left and right of the jumps with the keys 2 and 3.

BTW: the sequence the blue curve looks indeed, like it was shot im M, but there are some nasty peaks in the middle where you messed up the adjustment (false direction?) - maybe there is still one or more shots in this sequence where the mode dials was on A as well.

There was no time when it was out of M or Bulb.

The bad spikes are from where I had to stop a bulb shot in order to increase the interval between shots. Poor planning on my behalf, but not anything that relates to this issue.

I forced the HG button to enable by adding in all the 2* and 3* markers manually, which is a pain in the ass as this is one thing I expect LRT to do.

Can you double check where in the EXIF LRT is checking for the shooting mode? As I said, Lightroom is seeing it as M, but whatever is being used in LRT is picking up Auto.

It would be good to have a way for it to be overridden and reevaluate for exposure jumps.

Holy Grail approach in LRT ist not supposed to be used with Bulb mode. Since in Buld mode the Exif data is anything else then accurate. Maybe that Bulb shots are making LRT think that the sequence has not been shot in M. I personally never use Bulb because it just does not make much sense...
However, I will see, if I can add a way to override this detection in a next version.

How do you Bulb ramp over 30 seconds if you don't use Bulb?

Why would you want to use shutter times longer then 30 seconds for time lapse? Everything would run too fast, even the Milky Way. I never shoot times with shutter speeds longer then max. 20 seconds. Accelerating in post is never a problem. But slowing down is mostly ugly.

I want to go up to 1 minute when shooting stars on my 8mm fisheye, otherwise I don't get enough luminance from the stars.

You wont get more luminance with the long exposure since the earth rotates. I'd suggest increasing the ISO instead or getting a faster lens.

Sure, I get that, but with the 8mm a star barely moves through 1 pixel in 1 minute.