Not an expert on either the font or the history. The 18.104.22.168 release (https://software.sil.org/charis/release-v4-0-02-official-release/) page, however, says that “the Literacy fonts are identical to the main Charis SIL fonts, except that the default forms for ‘a’ and ‘g’ have been changed to those often preferred by literacy specialists – single-story ‘a’ and single-bowl ‘g’.” Your particular error message may (or may not) have been the result of “OpenType and Graphite features may not work as expected, and particularly those that interact with the Literacy Alternates feature.”
The question is why you are still worried about that specific version after 12 years?
There have been numerous 4.1xx releases since that time, and a major 5.000 release in 2016 (https://software.sil.org/charis/release-5-000/).
Even if you find those small number of literacy features absolutely necessary, I must still inquire why not try the 5.000 version of the Charis SIL literacy package (http://software.sil.org/lcgfonts/download/) ?
As a general response to your questions, it is my impression that Charis SIL is preferred for phonetic and phonological purposes these days. I used Doulos for awhile but ultimately switched to Charis because of this reason. Not sure about Andika, Gentium, etc. compared to it…someone else may know. Your question about the literacy package version of Charis SIL is the first time that I have even heard of the literacy package…so it seems that it is not widely used?
As for the regular Charis SIL, I’ve been using it on Windows 7, 8, 8.1 and 10 (versions 4.1xx and 5.000) since 2012 or 2013 without any issues. A fellow student of mine has been using Charis for approximately the same period - but at least since the 5.000 release. I’m not certain of his exact MacOS version, however.
It seems to me you should forget about the previous problem(s) and just try the current version. If you find you still have problems with the installation, then come back here and post the specific error message. The font experts will likely have more ability to help you troubleshoot then.