I have a similar background to you. All my previous sites have been hand-coded in HTML and CSS, more recently, with some simple PHP includes so I don't have to edit headers, footers and navigation menus on every page.
I'm still exploring what FlatPress has to offer and I, too, have little understanding of some of the things that Pingdom reports on. But my conclusion is that you should not take too much notice of any of it.
Here's the report on my first test page:
According to Pingdon my page has three 0 scores (rating F) and has fewer 100 scores than your page yet it's 3 times larger and loads almost half a second faster. In my book that's a satisfactory result.
The one comment I have about the code that FlatPress generates is that its stuffed full of "src=https://mydomain
" and "href=https://mydomain
" but I once read that its far more efficient to call relative addresses to avoid having to run through DNS each time you make a call to an absolute address. Maybe that's decade old advice that no longer applies, in the same way that once I was taught always to provide height and width attributes for images, so the page didn't have to re-flow as the images were downloaded. That was certainly true in the days of the Internet Explorer/Netscape wars but is most definitely out of date in the days of HTML5, CSS3 and mobile devices.