While it's false that having $2006 left pointing to the palette causes any problems, it's still true that palettes aren't buffered like other $2007 read/writes are.
The funny thing is that, even if the colour pointed to by the last palette write was to be used as background colour (this is not the case), then in most cases, the whole palette is written, so it'd point to $3f20, a mirror of $3f00. Even if only the BG palette is rewritten, $3f10 is still a mirror of $3f00. Only leaving the pointer at $3f01-$3f0f or $3f11-$3f1f would cause a problem, and those case would be very marginal.
So even if the take hypothesis that the last palette writen to is used as a BG colour was true, this "routine" would still be useless.
If the developers really tought they could use any colour as a background colour, they would eventually try this feature, and figure out that it doesn't work, isn't it ? If they did so and didn't change their code, then yes it's indeed cargo cult. If they just never tried anything else, we can't really call this cargo cult.
It might be useful to count licensed games that do write 3F 00 00 00 vs. games that don't in order to estimate how important this practoce was to Lot Check.
I'd be very interested in such a statistic.