if Myki is valid on the Frankston to Portsea service, then logically it should be valid on the Frankston to Cowes service as well.
The Cowes - Frankston bus only runs once every 2 weeks (!!) so while Myki may be introduced on it in the future the last time I spoke with the driver he wasn't aware of being able to accept Myki and - as per the timetable - would only accept pre-booked passengers anyway. As a public transport asset it's not exactly in the first league nor the most user-friendly of options. The 788 Frankston - Portsea bus is rather more frequent. And since when did logic and public transport co-exist happily?
Of the few people who might make the trip from Cowes at all often I suspect most would use the ferry and Stony Point train which offer 2 - 4 journey options every day. V/Line offers the main PT service for all points between Cowes - Tooraddin then continues to Melbourne with Z2 bus connections available at no additional cost (per V/Line ticketing conditions) via Cranbourne or Dandenong for Frankston.
No community is served exclusively by the Cowes - Frankston bus though it is the only service along part of the Baxter - Tooraddin Road.