I'm not ready to give up my use of the mk3 assembler, although I'll consider it. In the meantime, I have adjusted my use of pipe connections on the entity to, I believe, match pipe passthrough. This is my attempt to find a balanced solution that fixes the issue on both ends. Do let me know if it works!
Note that pipe passthrough actually makes the assemblers act more like a pump than a pipe (but a pump in both directions), and so this means that the same is now true of mk3 assemblers under this chemical mod. It's an interesting feature, I suppose.