Quick suggestion, not sure how practical it is or whether it would add unnecessary complexity, but I was messing with the following craft in the VAB today as an example:
Which initially fires all 3 engines, but then drops the outer tanks and low thrust Terrier engines. With crossfeed enabled on the radial decouplers and fuel flow prioritised to the outer tanks, the Terriers begin to consume fuel from the inner tank if I am not paying attention during a burn, rather than burn out. The workaround for me is to disable crossfeed on the decouplers and add 100kg of fuel lines.
I think it makes sense for the decouplers to have a 4-way switch, 'Off', 'Both', 'In', Out" (or up/down for stack decouplers), though I'm not sure if this would have a negative effect on the menu UI which outweighs its utility.
Also of note is that neither the KER mod or the stock dV readouts register an accurate dV unless the fuel line workaround is applied - I guess the code doesn't anticipate dropping engines which still have a fuel source.