would something like what Altium does (ie a graphical symbol denoting pairing) solve this?
additional metadata stored in the attributes of the nets that denotes what signals are paired
obviously not for v6, maybe not v7… although it would help with Altium imports.
Wich is one and the same.
There is a subtle difference, a beginner’s common mistake, although you are not a beginner at all.
William I. Fletcher “An Egineering Approach to Digital Design”.
But as it is nearly a philosophical aspect, let’s leave it like that.
For the “Inverted” versus “Asserted low”, I find the difference too small to make a distinction. It falls in it’s place when you use it depening on the meaning of the signal itself.
However, when you start adding double negation such as both a circle on a pin and and inverting bar you are creating confusion. According to strict interpretation you have an asserted low signal that is also inverted, and this is likely not the case. You should just never ever do that in a schematic. And similar with differential pairs. It does not make sense for both wires of a differential pair to have an inverting bar.
I don’t agree. A signal that is marked as negated is a logical function. A signal that is marked as asserted low is a reminder to me that when low the logical value of the signal is “TRUE”. As with everything else, context matters.
Yeah, you would probably hate my schematics because I use the “marked as asserted low” meaning on schematics so I would have a ~label going into a pin with a negation circle on it, and read it as: “This is a low active signal going into a low active pin. All is good, polarities match.” I don’t see it as the two symbols adding together like a truth table, I see it as each item (pin and wire) are separate and should match each other. I even have the names of the pins with negation circles with the overbar. Again, not as a truth table formula, but as complimentary documentation.
Yeah, remind me to never show you my schematics. 
This is perfectly sane and OK:
Take for example a wire with the label ~WR~ which goes to a pin with an inverting bubble. The Wire label ~WR~ indicates to the net that it is active low, and the inverting bubble on the pin also indicates that the chip accepts some inverted (cq. acitve low) write signal. It becomes an abomination if the text on the pin is also labeled ~WR~, because the bubble on the pin “inverted” the signal back to “normal”. Complimentary documentaton is OK, but be sure to not make it contradictory.
So now I’m not sure whether I want to see your schematics or not…
Yeah, this is definitely a point where we don’t agree. I don’t see the bubble on the pin as actually inverting anything. It is just saying “this is low active”. The overbar over the pin name just reinforces that the pin’s function is low active.
Agree to disagree?
But the bubble as an inversion is fundamental for the traditional inverter symbol. There, the signal is first buffered (triangle symbol (also used for amplifiers in general)) and then inverted (bubble).
It seems that KiCAD library people, too, mostly prefer single inversion: https://kicad.org/libraries/klc/S4.4/ (point 4.).
This is on the output pin, which is a whole different story to the discussion above.
I can agree you’re just as stubborn as I am but in a direction of ignoring sensible standards, creating faulty schematics that don’t work and creating confusion for people who see your schematics and have to use them for repair work.
But you’re not alone.
Not too long ago KiCad had a library for connectors with inverting pins.
There is no difference in meaning for the inverting bubble whether it’s used on an output pin or an input pin.
There certainly is no difference in meaning, but the output is totally dependent on the input so the problem of inversion or double inversion (depending on interpretation of signage of labels and/or input bubbles) doesn’t exist.
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