You would use “makes” when the subject of the sentence is singular. ... You use “make” when the subject is plural. Factors and other variables make the subject plural. You would use "make". Way to remember: Usually when the subject ends with the letter "s", it is plural. If subject ends with "s" use "make". If subject does not end with "s" use "makes"

No. As a stand alone sentence, "make" is correct. There is a possibility that "makes" could be used, i.e. if referring to the condition of there being other variables as a positive thing versus the alternative condition of there not been other variables, but it's a bit complex and unlikely.

You can say this way..... There are always other factors and variables, intangible sometimes, which really makes the difference. Avoid using ‘other’ more than once in a short sentence.

This is a little bit of a run on sentence. Try: "There are always other factors. Sometimes there are intangible variables that can make a difference."

"make" is correct as the factors/variables/intangibles are plural.