Is there an established method for comparing expression of groups of genes (gene sets)?
You could apply the GSVA transformation to later compare them. You would need to give a step back and start from the expression values not log2FC, but I think it would be better than using the log2FC directly.
If you need to use them you could compare the gene set enrichment value of these two sets on the same comparison. I would use fgsea with the log2FC and the two sets of genes. If the normalized enrichment value (NES) is different then you could explain that these sets expression are indeed different.