Installation around skylight workmanship questions

I have just had a standing seam metal roof installed and overall am very excited about it. However I am not feeling confident about the quality of the workmanship which makes me nervous about future leaks. My concerns are particularly about the installation of and around two new replacement skylights. From my own research of installation of skylights the work seems sloppy. When I raised my concerns to the contractor, they assured me it was all done properly, but I'm not sure. I'm not as concerned about aesthetics as I am that this installation will remain watertight.

To be specific:
1- panels both above and below skylight lie on top of the flashing

2- panels are bolted down on top of the flashing which I am not happy about as I chose standing seam to avoid exposed fasteners. When I expressed concern, the contractor told me that the fasteners will not need maintenance to replace the rubber washers.

3- There is not 6" of space between the skylight and the seam on one of the sides of one of the skylights (I had read that this is the recommendation/standard).

4- There is a large gap between panels on one side (it seems they had to cut one of the panels mid-way down for the installation). It looks like in a storm water could blow up under the panels. They seemed to rely on a lot of caulking to seal up the areas where there are gaps.

I am looking for a second opinion on their answers to my concerns. Perhaps I am just being too worried and the work is in fact done well. I will upload photos of the work here. (Note-- these are photos of two different skylights-- both have issues with the bolts and placement of flashing, only one has the issue of closeness of the seam as well as the panel being cut midway down the length).

Thank you so much for your response! I contacted the manufacturer and they told me they do not do inspections of work. However I will try to contact them again. Perhaps they could answer specific questions such as this even if they do not inspect work done. I really appreciate your help and quick response!!

Update: Thank you again for your support. I contacted the manufacturer to share my concerns and photos. They confirmed that work was not done properly and contacted installer directly which led to a response. They will be re-doing the install of the flashing which will involve replacing 6 panels around the skylights. New installation will not have exposed fasteners. After they have completed the work I would like to have the whole job inspected (since there are many areas of the roof I can't see without climbing up there) and I feel I need to do that for peace of mind. Manufacturer told me that they don't do inspections and they didn't have a contact for me in the area. Do you all have contacts of a reputable contractors in the eastern PA area (I'm just outside Philadelphia) who I could reach out to for an inspection?

I recommend that you contact John Diffenbaugh. He is an independent metal roof consultant.
[email protected]
717-545-7943 office
717-579-9926 cell

Thank you so much for all your support. It has been incredibly helpful!

Thank you so much for your support! John Diffenbaugh is fantastic and has been so kind in making time to help me. Unfortunately, he identified numerous problems I hadn't recognized as issues and confirmed that other areas that I felt uneasy about are in fact not done according to the manufacturer's specifications. This includes a valley that needs to be re-done, using only one fastener in the middle of the panels as a top anchor and no use of butyl tape seal at any of the zee closures. In his opinion, the roof panels are not secure enough to hold the solar panels that I have purchased that await installation in my backyard. The contractor has dismissed the inspector's report and questions his qualifications and are demanding payment, claiming that they have completed the work. In my view it is not complete if not done according to specifications, but this is an agonizing situation and I'm not sure what to do next.

Sorry for delayed response Christy, I'm attaching a photo of Velux solar skylights installed with standing seam. I reviewed the photos you posted, your skylights were poorly installed. Standing seam and any required flashing components should interlock with skylights, or any other additional accessories you choose to incorporate with your standing seam metal roof. Using exposed screws defeats the purpose of spending the extra money on a standing seam system. Hopefully your current roofing contractor will make the corrections in a reasonable, timely manner. If they do not, I would recommend making use of the Metal Roofing Alliance's "Find A Contractor" section.

@Patrick McDonald your photo did not come through in the posting. Could you repost?