Hi,
This is my take on it;
As you have correctly stated, there are two lists:
SEM list -
https://www.sem.admin.ch/sem/en/home...countries.html
FOPH list -
https://www.bag.admin.ch/bag/en/home...nde/liste.html
The primary list is the SEM list, if the country isn't on the list of allowed countries or 3rd country exceptions, assuming you are a national of that country, you cannot enter Switzerland without a valid work, residency or special occasion permit.
The secondary list is the FOPH list, this determines cases whereby you will need to quarantine.
A couple of examples:
If a country is on the SEM list, but also on the FOPH list, then you can come in from that country but you'll need to quarantine.
If a country is not on the SEM list, and not on the FOPH list, you cannot come in from that country.
If a country is on the SEM list, and not on the FOPH list, then no problem you can come in without quarantine
I hope this helps, the only caveat I'll throw in there is that if you're currently a citizen of a Schengen state then it's also ok to come in, but be careful which country you're arriving from as it may have quarantine requirements.
Also, having a permit e.g. D, C, B etc. only permit entry, it doesn't remove quarantine requirements per the FOPH list.