Answer: Yes, native speakers emphasize the be verb when they want to emphasize them.
When the verbs are action verbs, one would stress the auxiliary:
- But he did do it.
- In fact, she does know them.
When the verb is be, the verb can be stressed, yes:
- But in fact he was there. I saw him.
- Sure, they were playing football.
Why would these be stressed? Because there are implied ideas:
But in fact he was there. [Another speaker had been saying he was not there]
Sure, they were playing football. [Another speaker said, they are playing it now.]
These are emphatic uses. With action verbs, the emphasis is from the auxiliary. With the verb be, it can only be heard, not seen. Therefore, in writing, to signal it, one must use italics.
- But in fact, he was there.