Did somebody say
flagchat?!
Anything in a spoiler is a suggestion for the country named in bold above the paragraph above the spoiler.
Czech Kingdom
Below is the coat of arms of the Kingdom of Bohemia on a red background. I can see a monarchy harkening back to the old days of the Czech Bohemian kingdom, and there's no need to appease minorities here.
Euskadi
I have three alternatives for the flag of Euskadi. Basque nationalism is a relatively modern invention (the 1890s) OTL so its hard to find ancestral flags of the Basque people that aren't just the flag of Navarre (which you can't use because thats pretty explicitly a monarchist symbol and generally Carlist overall.) So here are a few attempts at an alternative. The first is the traditional (as of 1891) flag of the Basque region.
Below is one of the variant flags designed by the same guy who did the above flag, which is hilarious because it craps all over rule of tincture and looks awful.
Finally, we have the asserted flag of all Basque peoples (in both France and Spain), which I can't find much about. But it has an eagle on it.
Galicia
Below is the 1845 Naval flag of La Coruña, from which the modern flag of Galicia comes from (they removed one arm of the cross.) Galicia does have a flag of its own, but it was changed in 1891 due to the fact it was confused with the Russian Naval Jack and then changed again to add a coat of arms. This would not occur in this TL (since the Russian flag is noticeably different and has a bear) so the flag would probably be maintained without alternation.
Botswana
Botswana is the term for the territory of the Tswana people, who historically prior to British colonisation did not have a flag. However, during apartheid South Africa did establish a Homeland for the Tswana people, which did have a flag. Below is the flag of the Bophuthatswana Homeland.
Below is the flag of the Bophuthatswana Internal Intelligence Service, which I added because its hilarious and has a skunk on it. And who doesn't love skunks?
Hashemite Sultanate
Below is the historical flag of Hashemite Hedjaz, which not only occupied the same area as the Hashemite Sultanate but was ruled by the same people. The following design appears on all flags of Hashemite-ruled states, with minor differences (such as the addition of stars on the Jordanian and Iraqi flags, and a crown onto the Kingdom of Syria), implying that it was a royal Hashemite standard of some kind.
Mali
The traditional Pan-African coloured flag (red yellow green) in use by much of north and western Africa is a modern invention, disqualifying Mali's current flag or its variants. The Kanaga, the human-like symbol that was on the flag of Mali in the early sixties is also a modern invention, I believe. Below is a possible flag of Mali in this TL, that being the banner used by the Mali Empire in the middle ages.