Exposed underlayment

There was a small leak in my metal roof and I called a roofer to address it. He said he would need to remove the metal panels, remove the old underlayment, place new underlayment, and replace the panels. He said he would use new screws that were slightly larger, placed through the same holes so it would seal. After the job was done, it was clear he did not put the panels back on the way they came off. He said it is impossible to do that. Because of this, I counted 26 holes through the metal where the underlayment can be seen. He says it doesn't matter because the underlayment is what keeps the water out. This does not sound completely correct to me.
Many of these holes are just below the peak, so water will travel all the way down the roof under the metal during the winter. I am concerned. Am I wrong?

Thank you. As a follow up question, is it typical to put the metal panels back in a different configuration? He says it is not possible to put them back in the same configuration they came off and it is therefore not possible to use the holes that were previously there for the screws.