I saw this and pinned it for later but knew it might be a problem. I think I found a work around. In the distribution target setup there is a setting call "Publish only Incremental changes for a modified assembly when publishing a BOM". Changing this to "no" shifts the components to added only but had the effect of displaying all the substitutes. You have to give up the incremental but in my case, we were deleting the BOM lines and re-adding each time. Do you think there are downsides to using this setting I might not be seeing?
I opened up a case on this with PTC. Our integration depends upon setting incremental changes to yes so I am forced to choose to lose subs in the process of a changed BOM. I've asked PTC to re-examine issue since it results in a loss of BOM information in transit and there is no good reason for it. Short of that, if I find a way to alter PTC default code, I will post a patch to fix this here.