Those regions don't have flags, so I'll give some proposals. The number of proposed regions in continental Portugal is variable, but I'll consider the seven below for this post:
Seven is more flags than the average by post, so I like some of the flags below more or less.
The first flag I created was to Beira Interior. It's based in the flag flown by the Lusitanian leader Viriatus, that resisted to Roman conquest until his death, in 149 B.C. It's claimed that the flag consisted of a white cloth with a green two-legged dragon. Later, the green dragon became a Portuguese royal symbol.
Other region with a easy flag is Algarve. For long, the title of king of Algarve was subsidiary to that of king of Portugal. Some medieval heralds have attributed arms to the titular kingdom, consisting on a quartered shield with the heads of Saracen and European kings. the other of the heads and the field colors varying.
Firstly, a design with a more contemporary representation, and the armillary sphere from the current flag of Portugal:
Other variation I considered was a banner of arms, with a more Medieval depiction:
The flag of Entre Douro e Minho ("between Douro and Minho rivers") is punning: Douro sounds like "d'ouro" ("of gold"), and a possible etymology of Minho is "red" or "vermillion". The position of the stripes represents, more or less, the disposition of those rivers.
Following, Trás-os-Montes e Alto Douro ("behind the mountains and higher Douro"). I used the same symbolism for Douro, and the green mountains represents the name of Trás-os-Montes and some of its geographical features. I later noticed that the green mountains forms a "M" of Montes ("Mountains"). A curious note is that I have some ancestors from this region of Portugal.
For Alentejo ("beyond the Tejo river"), I designed a flag featuring the yellow of its large camps and the blue of its sky. The darker blue stripe represents the Guadiana river, that divides Portugal and Spain, and where the biggest dam of Western Europe is located.
For Estremadura e Ribatejo ("bounds of Douro and above the Tejo"), a white stripe representing the estuary of Tejo river, with black and white representing Lisbon and purple and white representing Setúbal.
For last, the hardest flag to be design, to Beira Litoral. You can see it below:
The blue cross on white represents the medieval County of Portugal, that would later gives origin to the kingdom of same name. Black and white are the colors of the traditional costumes of the University of Coimbra, one of the them oldest surviving European universities.
Comments are welcome.
The chosen map does not necessarily means I endorse it.