If I understand correctly the original QS tradition was to spell as you speak, apart from some general principles, most importantly to spell out all R's. The manual reflects Reed's pronunciation 60 years or so ago, and it is only natural that pronunciation differs in time and space (including social space). When you write only for yourself there is absolutely no reason not to spell as you speak. Most modern people get freaked out by lack of or difference in spelling standard because schoolmasters have succeeded in making people think they are stupid if they don't master traditional orthography. That's one of the things which Quikscript was meant to get away from. If you are going to write "phonetically" people will necessarily spell differently because people pronounce words differently. That was perfectly normal for most of human history. The idea of a standard spelling only emerged in the 17th century.