Immunity is specific to the testimony you give.  

If Michael Flynn gives testimony with specific immunity and someone wants to punish him, they would simply prosecute him for 'trumped up' charges based on something other than that testimony.  No immunity can protect a person from false charges if someone is determined to do that.

A grant of immunity is, however, effective is in protecting you from conviction for the crimes you're going to give evidence on.

So no, there really is no reason to seek immunity if you don't think the evidence you're about to give has a good chance of leading to your conviction.  The reasons to grant immunity are clear - his evidence will lead to the conviction of someone even more important.