Fix compiler warnings in Zephyr and FlexPRET support files

[erlingrj]

See title.

[erlingrj]

This PR addresses some new compiler warnings that arose when we changed the FlexPRET compiler. It triggered me to change a little the atomics API. I removed the functions explicitly targeting int32_t. Because it is used on many variables which are of type int and then they need to be casted. What is really needed is to have an atomics API capable of modifying 64bit values.

There is a test failure on FlexPRET, this is because reactor-c CI is referring to the CI jobs in master of lingua-franca, which is outdated. It will pass when we merge: lf-lang/lingua-franca#2405

[edwardalee]

Looks OK to me. I added three questions.

[erlingrj]

@edwardalee thanks for the review, sloppy of me to overlook the missing int32 -> int update. It is done now and I did a final self-review. Will merge when issues with the corresponding PR in lingua-franca is solved.