The question/answer section of the preventive control rule touches on this slightly when discussing R&D plants:
In general, a foreign or domestic facility that manufactures, processes, packs, or holds human food for consumption in the United States and that has to register with FDA under section 415 of the Federal Food, Drug, and Cosmetic Act is subject to the requirements related to preventive controls (primarily located in subpart C and subpart G) of the Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Human Food rule (21 CFR part 117; 80 Fed. Reg. 55908) (CGMP & PC rule), unless subject to an exemption (see 21 CFR § 117.5 for exemptions). Note that an establishment may also be subject to the Current Good Manufacturing Practice (CGMP) requirements in subpart B; those requirements are not dependent on whether a facility is required to register.
If a research and development (R&D)/pilot plant or test kitchen is a facility required to register (see 21 CFR § 1.225 , it will be subject to the requirements of the CGMP & PC rule, unless an exemption applies (see 21 CFR § 117.5 for exemptions).
In the rule itself, it looks like non-registered facilities are defined as "mixed type" but then they go on to only use the term in reference to farms, so unhelpful there.
I can't find anything in the actual law stating that registration status has any impact on which portions of the law you must be in compliance with, just references that registered facilities are only exempt if they fall under one of the exemptions.
I would treat the two categories separately. If your facility handles food, and works in interstate commerce, then I would operate under the assumption that you need to look at the exemptions listed under each FSMA final rule for it's applicability, independent of registration status. Basically everyone assumes that if you had to register, then you fall under the rules unless an exemption applies. But if you didn't have to register you likely fall under an exemption, but registration is not a prerequisite as to whether you fall under the rule (at least according to the law as written, FDA guidance may state differently).
Note that FDA and amazon are currently having a fight over the retail exemption, so this is going to be grey area as long as FDA doesn't bring the hammer down on that particular dispute. I interpret the stand-off there being that amazon is "technically" correct in their interpretation of the law, but FDA expects such facilities to register regardless.
They have a confusing note on this final rule page:
Registrations are now required to contain the type of activity conducted at the facility for each food product category. This will be required when the final rule becomes effective on July 14, 2016. The final rule also amends the definition of a retail food establishment in a way that expands the number of establishments that are considered retail food establishments, and that are therefore not required to register with the FDA as food facilities. However, all food establishments, including retail food establishments, continue to have a responsibility to ensure their food is safe.