The short answer is yes, they are pronounced the same. But "Boss' car" is not the correct use of the apostrophe.
To show possession in the singular, you add apostrophe + s. So your first example is correct: "my boss's car."
To show possession in the plural when a word ends with s, you add the apostrophe at the end. But the plural of "boss" is "bosses," so it would be "the bosses' car."
"Boss's car" and "bosses' car" sound exactly the same.