The text size of pages can be changed, smaller sizes fitting more text in a given screen space but larger sizes being easier to read. By default each page has its own controls that set the size for that page only and for the current device only. Setting a system-wide fixed size for all pages and all devices here will remove those controls from each page.
Your browser has a built-in baseline font size it uses for all sites, and this is considered the medium font size in BibleStudy.tools, the other sizes going up or down from there. Some browsers let you set this baseline size, and if you do this you set the BibleStudy.tools medium size and the other sizes follow along. Some browsers have different size settings for different types of fonts, and if your browser has a "monospaced" or "fixed width" size then BibleStudy.tools will use that as its medium.
Note that any sizes you set using the page-by-page controls are automatically remembered, but only if you're logged in. If you're not logged in each page goes back to medium when it's reloaded. Also, if you set some page-by-page sizes, then later set a system-wide size here, your page-by-page settings are ignored but not forgotton: if you turn off the system-wide fixed size then your old page-by-page sizes will be used again.
The tools/Generate page sends a message when it begins a PDF generation batch, and again when when that batch is done. By Default these messages go to your screen if you're logged in, and to your email otherwise, but that can be changed here.
If you want to always open the Notes panel when clicking on a verse in the Chapters panel, turn that on here. It can be more convenient to open notes this way, but it can also open them when they're not wanted. For example, if you triple click a verse to select it for copying, you probably don't want that first click to open the Notes panel.
Likewise, if you click on an old note in the Notes panel it's pulled into the Edit Note area, but by default only if the Edit Note area is already open. The same is true when notes are focused on a study and you click on a verse in the Chapters panel. If you want to always open the Edit Note area in these cases, turn that on here.
When you type a note or a study text some special editing features are enabled by default. These are described in the help on the tools/Chapters page, under the "Edit Note" section. They can be turned off here.
When the tools/Generate page creates PDFs it hyphenates to reduce white space between words, which also reduces so-called "typographic rivers" that can be a distraction while reading. However, hyphenation breaks words at the end of a line, which can itself be a distraction. By default hyphenation is allowed to break only compound words where each part of the compound has at least three letters, and each part is also a stand-alone word in the Bible. More aggressive hyphenation is enabled here.
For example, by default the word "bondservant" might get hyphenated, putting "bond-" at the end of a line and then "servant" at the beginning of the next line, because "bond" and "servant" are both standalone words in the Bible. However, it can't by default be hyphenated as "bondser-" and then "vant" on the next line. Aggressive hyphenation allows this.