I don't know much, but if Don Carlos had a son, does that mean that Portugal is now more united to Spain?
Portugal was already attached to Spain. Too many marriages between both countries.
Charles had his claim to Portugal, but also Phillip (Charles's father) had his claim to Portugal as well. Father and son are children of Portuguese infantas.
Charles has the claim of his mother (Princess Maria Manuela of Portugal) and the claim of his father (son of Infanta Isabella of Portugal).
The only difference is that Charles (Phillip's son) had a greater "claim" than Phillip, but that doesn't really change things (Portugal is inherited by Spain).
Succession of Portugal (~1578)
King, Sebastian I of Portugal (grandson of John III of Portugal, son of Prince Joao Manuel of Portugal)
A) Offspring of King John III of Portugal (grandfather of Sebastian)
1) María Manuela of Portugal (dauther of John III of Portugal). Heir presumptive between 1527 and 1535. Married with Phillip II of Spain.
2) Charles of Asturias (son of Maria Manuela and Phillip II) (OTL he died, childless).
3) Charles II of Spain (son of Charles)
B) Offspring of King Manuel I of Portugal (father of John III of Portugal)
4) Henry of Portugal (son of Manuel), a cardinal. Childless.
5) Duarte of Portugal (son of Manuel), Duke of Guimaraes. Married with Isabella of Braganza He died.
6) Duarte of Guimaraes (son of Duarte), Duke of Guimaraes. He died, childless.
7) Maria of Guimaraes (daugther of Duarte). Married with Alexander Farnese of Parma, Piacenzia and Castro. She died.
8) Ranuccio I Farnese (son of Maria), Duke of Parma , Piacenzia and Castro.
9) Others childrens of Maria of Guimaraes.
10) Catarina of Guimaraes (daugther of Duarte) Married with Joao, Duke of Braganza.
11) Teodosio of Braganza (son of Catarina)
12) Others childrens of Catarina of Guimaraes.
13) Isabella of Portugal (daugther of Manuel I of Portugal). Married Charles V of HRE and I of Spain.
14) Phillip II of Spain (son of Isabella).
15) Children of Phillip II
16) Maria of Spain (daugther of Isabella). Married with Maximilian II of HRE.
17) Children of Maria
18) Beatrice of Portugal (daugther of Manuel I of Portugal). Married Charles III of Savoy.
19) Children of Beatrice.
I omitted some people who are dead, and more than half that I mentioned are dead.
The Portuguese throne (OTL, if Charles of Asturias died childless) was to be inherited by Henry, the cardinal.
Then by the Farnese, descendants of María de Guimaraes. And then by Catarina de Guimaraes, and the Braganzas (children of Catarina).
Unfortunately the Farnese did not have much influence in Portugal and were surrounded by Spain. To make matters worse, Catarina wanted the Portuguese throne for her and her children, and she had the power and influence of the Braganzas.
With a claim "divided" between the daughters of Duarte, it was easy for OTL Phillip II to take the throne after the death of Henry, the cardinal.
PS: In my opinion, Portugal would be independent if María Manuela has a daughter. A daughter who inherits Portugal from her mother, but not Spain (Phillip has sons with another wife). I doubt that Phillip will steal the inheritance from his own daughter.