Sure, of course the different multicellular eukaryotes vary, but the diversity is very low compared to what we see across all life, look at Figure 1 here for example [1].

I am looking at it from the perspective of the structure of the metabolic network, as this is my area of research. There is a huge amount of diversity in the fundamental structures of metabolic networks, types of metabolites and enzymes produced, etc. across all life, but from that perspective the differences between one multicellular eukaryote and another are slight in comparison. Multicellular eukaryotes have evolved very different behaviors, shapes, sizes, etc. from a relatively conserved biochemistry. When taken out of the context of an organism in cell culture, the cells are similar enough that their behavior under diverse experimental conditions can be predicted by nearly identical metabolic models, whereas you would see nothing of the sort with distantly related bacteria- the metabolism can be massively rearranged.

[1] https://www.nature.com/articles/nmicrobiol201648