Flashing Metal Chimney Pipes

I started putting on a standing seam metal roof over our shingles this January. A little here, a little there, but so far so good. I'm 2/3 done and we love the way it looks.

Now, however, I'm down to the end that has two chimney pipes from wood burning fireplaces poking through. I think these must be "type A" pipes because the fireplaces are wood burning.

What is the best way to flash these pipes? Can I just use a plain EPDM rubber boot or do I need the high-temp silicone boot? Is there a better way?

Any thoughts are appreciated.

Thanks.