A grammatic question about modification

You question seems that you wonder why "not" can't modify intelligent.

"not" is an adverb which likes verbs such as is/are/was/were/have/has/must/can/could/shall/should/will/would/may/might/do/does/did

"not" is combined with these verbs to form a negative meaning. (is not, was not, have not..., etc.)

"not" also comes after some verbs like "hope", "believe", for example, "I hope not" or "I believe not" when you reply to someone's question like "Is the man coming?"

If you make a negative meaning with "a not intelligent boy", you could use prefix "non" which has a negative meaning: a nonintelligent boy or a non-intelligent boy

British English likes using -(hyphen) more than American English does.

For your grammar, as you can see "He is not an intelligent boy", "He isn't an intelligent boy", "He isn't a very intelligent boy", if "not" is used in a sentence, it becomes a linking verb which needs complements such as a noun, adjective and the word order is like this: a/an/the+(very)+adjective+noun or just a single noun with an appropriate indefinite article of "a" or "an", or definite article "the"

For your info.

He is intelligent (O)

He is not intelligent (O)

He isn't intelligent (O)

He is intelligent boy (X)

He is not intelligent boy (X)

He is not an intelligent boy (O)

He is a not intelligent boy (X) > "a" isolated "not" from "is" (divorced)

Now "not" does not function as a verbal negation and can't directly modify attributive adjective like "intelligent" in an example you gave.

So, "a not intelligent boy" is no good(grammatically wrong).