You can also use the bucket o meter to measure the fluid drum amount and then use redstone signal to turn a garbage can ON/OFF based on how much fluid the drum has. But I have to say that the solution with the pipe and valve is simpler. I tried to use that some time ago as well and I got some problems just like you did as I did not put multiple pipes there so that when the pipe emptied it lost the filtering function (and started voiding things that I did not want to void). I also remember that it used to work to put the valve between two pipes to make it work like a one way valve between those pipes, now you need to put some container between or use the fluid extender.
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