Was there any rhyme or reason as to why early Moldvay and Cook basic and expert sets came with dice all of the same color, or dice of different colors? Did the different colors come first due to some shortage or later? Or were these just the rest of using what was available at the end of the day?

I ask because I am struggling with which I prefer. Dice of all the same color seem to make more sense. Dice of different colors could have been original, or put together from other sets. Sealed dice of different colors dont appear as commonly though. So, thats kinda cool.

I am more concerned about ensuring my set is as-was. I wasnt really playing until the red box days.

So for Moldvay sets, they shrink-wrapped in-house at the TSR warehouse, and the sets all initially matched. When they got to the end of stock, they'd mix colors.
For Mentzer, they were wrapped by the manufacturer, again in matched colors until they got to the end of stock.

I have seen mixed sets in plastic of both types, though Mentzer seems less commonly mixed, and usually only with a couple colors... where I've seen Moldvay with 4 or 5 colors in one bag.

I hear that international boxes were also VERY mixed (boxes and books mismatching was not uncommon, much less dice).

I hope that helps.

Thanks for the validation Dan.  Welcome to The Acaeum!