I think workbenches would be clearer if connections of disabled transformers became hidden by default.
I realise it's only a right click away to show/hide the connections on the transformer but this seems a useful addition.
Maybe a new entry for the Options -> Workbench -> Transformer Options
Alternatively have the connections also disable so they grey out, so you can still see how the disabled transformer fits in, without the connections interfering with the rest of the workbench.
+1The issue here would be if you did have a mixture of disabled and enabled connections
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