PMMail doesn't actually use those settings for anything, and it doesn't matter if they are set, or not, unless you also use the available PMMDiags package (for extra logging). Then, it is used to find the location of PMMail (forcing the user to do the setting, if they want to use the package).
The bottom line is, that few, if any, apps actually use that stuff, so there has been little incentive for anybody to bother.
Why the "if any", when you report that PMMDiags "actually uses that stuff"!? I don't know why PMMail on its own would ever "actually use those settings for anything" anyway, unless such an app would be some extension of PMMail.
A bothered developer or bothered users, a rather clear choice. Presumably you cannot control the number of "apps actually using that stuff" of remaining users of PMMail, and unfortunately the install procedure of an OS sets a different default e-mail client. So the competition, pleased users, integration of an informal and unannounced new OS standard, the simplicity, and e.g. a possibility to synchronize known inboxes can be some incentives for quite a few developers.
BTW: of course anyone has the full freedom to write a fully open default e-mail client installer, a more aggressive installer for a single product, or perhaps even an uninstaller to delete an alleged useless setting. I won't write an open one, for example because I had to pay for my copy of PMMail, it's not as easy as setting a default browser, and e.g. MAILTO.EXE and YARN.EXE are e-mail solutions which may be hard to integrate.
Either way the on-topic installer won't enable a change by default. So the user has to enable, confirm and apply it intentionally. A specific warning could be possible, but apparently users of PMMDiags had to set it earlier. They should be able to recognize their own explicit setting, which will be displayed. In theory PMMail, or a new QT 5-based browser, can be included as an adopted member of the Mozilla family too, but it's not a fully open installer. For one due to its links with the MozTurbo-solutions.
As such the setting does affect the code significantly, but I'll include it because IIRC it was one of the original requests and other apps can and will use such a new "OS" setting. Yet another component of ArcaOS available as an "informal upgrade" for OS/2 and eCS: a default e-mail client setting.