Maybe other intelligent life forms don’t make the same assumptions that we do that lead to the statement that there are two “apples,” and maybe mathematics isn’t universal.

That just shows that "Apple" isn't necessarily universal, and doesn't actually disprove the universality of the concept of "two."

There are a ton of different physical ways to represent the Fibonacci sequence, for example, and I would imagine the first contact looks for ways to find the mutually understood medium by both sides: raised symbols, pulses of radiation, pulses of vibrations, physical pebbles arranged in a line, physical pebbles manipulated over a timeline, etc.

Once we establish a common medium, we'd explore mutual understanding of prime numbers, approximations of pi/e/phi, and things like that.