EV 150 specifies what gets penalized (e.g. it has a detailed description of what constitutes a run out), but does not say how many penalty points go with each.
EV 153 specifies how many penalty points go with each fault (e.g. 4 points for the first disobedience)
Yes, they could have just put the Compulsory Retirement stuff in 153, not 150. My guess is that they wanted to put it in both places so no one would miss it.
With regard to imposing the CR penalty even when SJ happens last, this was discussed in detail at the (virtual) rules change session at the (virtual) USEA Annual Meeting (and should be available on the web site). The rationale (and I am not saying I agree with it, just explaining it) is to be “fair” with regard to year end awards (NOT for safety). If the CR were ONLY applied when SJ is first, then a rider with 20 SJ jump penalties in a D-XC-SJ HT would finish wilth score (and possibly a placing if the division were small), and the rider with 20 SJ jump penalties in a D-SJ-XC HTwould finish with a letter (and no placing). This would give the first rider an (unfair?) advantage in any kind of year end standing