Structural zeros and multi group comparisons

[MarieBraadLund]

I have been running ancombc2 where I compare three groups A, B, and C. I wish to make all three comparisons (A-B, A-C, and B-C) and have run the code with and without the 'pairwise' option to obtain this. Regardless if I run it with or without the 'pairwise' option I run into the same problem with structural zeros:
If taxon_1 has structural zeros in group A, but is present in group B and C, then taxon_1 is not included in the differential abundance analysis. This makes sense when I compare group A and B or group A and C, but I don't think it makes sense when I compare group B and C where taxon_1 is present in both groups. However, this is what happens: taxon_1 is not present in the res output if it has structural zeros in just one of the three groups.
Is there an option to solve this issue? or do I have to run ancombc2 on two groups at a time to get the full analysis done?