Here are the answers to your questions:

1. Most journals have different specifications for different article types. Please carefully read the journal guidelines and set the manuscript format as per the article type. Ensure that you select the right article type in the submission system. Usually, the format of the PDF is pre-set by the journal and depends on the type of article. The PDF might also include additional elements like page and line numbers. Please check all the above points and if you still think the PDF format is incorrect, you should email the journal. 
2. Regarding the figures, please follow the journal guidelines for figure formatting in terms of size, resolution, and artboard size. These mismatches can often lead to AQC errors. If you are sure that the figures have been formatted to meet journal requirements and the AQC report is not a fail, you can go ahead and complete submission. You can either mention the artwork issue in your cover letter to the journal or send an email to the journal via the submission system.

Related reading:

• Manuscript submission checklist: Everything you need to consider before submission
• Discrepancy between instructions on journal website and submission system: A case study