Q Why might pumpkin scones made on butternut pumpkin (even the smell) made someone with Irritable Bowel Syndrome [IBS] feel ill?

A Smell is usually a good guide to tolerance. Reduce the amount of foods that smell ‘too strong’. But if the pumpkin is tolerated as a vegetable there must be a texture/density factor that is making the difference. I presume they were home made? If normal scones are tolerated then try different levels of dryness in the cooked pumpkin.
Often it is probably not the ingredients but the final product. Look at the nearest tolerated product and see if you can work out the texture, density, stickiness and moistness difference to work in your favour. It is also a good idea to have the frequent sips of water with food eaten. This reduces the density of what enters the stomach.

Q Should you have the diet strict enough to prevent pain, discomfort, and feelings of noticing a difference, in order to maximise benefit from diet effort.

A It is fair enough to be annoyed with those who criticise food sensitive people by saying that they are “over-noticing” symptoms. I have met siblings where one has a very high threshold to pain and another a very low one. It is good or bad luck which one you are. The pain is being felt and worth adhering to the diet to minimise. However sometimes it is worth a bit of resulting discomfort to enjoy some food. Each supersensitive person needs to work out just where they are at in terms of discomfort versus diet restriction. There is no evidence that relaxing the diet, and having some discomfort sometimes, is harmful to the gut as recovery seems so good.