I am an engineer qualified under the FRA rules and have worked for shortlines that included running on trackage rights over Class 1 railroads.
The FRA rules for non-common carrier railroads (such as the Loop and Sumpter Valley) are somewhat different. According to 49CFR part 209 Appendix A ... "If a tourist operation off the general system is insular, FRA does not excercise jurisdiction over it, and none of FRA's rules apply. If, however, such an operation is not insular, FRA excercises jurisdiction over the operation, and some of FRA's rules (i.e. those that specifically apply beyond the general system to such operations) will apply. For example, FRA's rules on accident reporting, steam locomotives, and grade crossing signals apply to these non-insular tourist operations (see 49 CFR 225.3, 230.2, and 234.3) as do all of FRA's procedural rules (49 CFR parts 209, 211, and 216) and the Federal railroad safety statutes themselves."
"In drafting safety rules, FRA has a specific obligation to consider financial, operational, or other factors that may be unique to tourist operations. 49 U.S.C. 20103(f). Accordingly, FRA is careful to consider those factors in determining whether any particular rule will apply to tourist operations. Therefor, although FRA asserts jurisdiction quite broadly over these operations, we work to ensure that the rules we issue are appropriate to their somewhat special circumstances."(excert from the 2005 edition)
Bottom line: The FRA does not necessarily apply all its rules to a tourist operation off the general system of transportation. It seems they usually fully apply some of the rules to address specific areas. The full requirements for qualifying engineers under FRA rules does not seem to normally apply, the FRA apparently finding the railroad's existing training and qualifications sufficient. But, the FRA reserves the right to change its mind at any time if there is a safety concern and fully apply the approriate rule.
