None of the depictions in your photos are right. Good call.
Try this link:
I know it’s from a copper site but the diagrams show proper installation details. I use these links for many metal roof examples for clients and builders. A picture or diagram simplifies explantions.
Flashings are designed to be the moisture barrier for penetrations and go under roofing material on the high side and over roofing material on the low side, just like shingles. Ribbed roofing requires specially constructed ribbed flashing.
Sealant of any type for any application should never be considered as flashing material or permanent moisture barrier. IT WILL FAIL and needs to be monitored for removal and reapplication, this rarely happens before a leak occurs.