This is actually a deliberate change to allow the new "Give new objects the most recent attributes" (GNOMRA) option to work better. This change avoids quite a number of anomalies with brush colour handling. Any newly applied brush is applied in "local colours replace: named brush colours" mode. However, if you pick up a brush from an existing line (and with GNOMRA switched on that is as easy as just clicking on the line), then its colour replacement mode is used for new brush strokes, so you really only have to change the colour mode once to suit your needs and then pick the brush attribute up from existing lines before drawing new strokes.
I do not think there is any disadvantage compared to earlier versions. Previously, the colour replacement option of newly applied brushes was always "No colours" and you could not change that in the brush definition either, so it was stuck, too, just to a different value. So, this is just a change of default value. Yes, it is different, but as far as I can see it does not lose anything.
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