I still struggle with really understanding the flow of minimum equipment, but I'll take a stab at it and see if I'm understanding it correctly.
To the point of 91.209, the plane doesn't fly at night regularly so that shouldn't be a problem (at least I wouldn't for this reason).
Going through 91.213(d) I pulled up the Type Data Certification Sheet and it if I'm reading it right it says for equipment: "The basic required equipment as prescribed in the applicable airworthiness regulations (see Certification Basis) must be installed in the aircraft for certification". Which would lead me to 91.205(b) (TOMATO FLAMES) which says the beacon is only required if certified after 1996. So that seems ok.
However just pulling up a random POH I found online to look at its own equipment list it says:
Flashing Beacon - 33-04-S
Anticollision Strobe Light - 33-05-R
This is where it gets gray for me as I'm not sure which of the above the beacon falls under and if the "S", being standard equipment means its required or not.
However this is the first time I've ever read 91.405 (thanks for pointing that out) and I'm with you there, that they really should be replacing it as it goes for its annual and 100 hours.
(Sorry for hijacking)