I regularly commute from Slaithwaite to Manchester, so I've been round the block a few times on the best Season to get. Until a negative easement was introduced last year, it was cheaper to book an 'Any Permitted' season from Halifax than from Huddersfield, and this was valid via both Hebden Bridge and Diggle. I believe this same easement now also forbids travel from Brighouse to Manchester via Huddersfield.
1. The West Yorkshire and GMPTE zones do meet as shown on the maps at The Great Western (Standedge) so you can use Zonal Tickets for through journeys by bus. However he rail line between Marsden and Greenfield is deemed to be outside both West Yorkshire and GMPTE zones, and the fare between the two is dreadfully expensive compared with WY and GMPTE tickets. The stoppers are pretty empty through Standedge Tunnel, as many commuters west of Huddersfield drive across to Greenfield or Mossley so they need only GMPTE tickets.
2. There are separate fares 'Any Permitted' and 'Route Hebden Bridge' and 'Route Direct' to Manchester Stations. ('Route Direct' tickets for Slaithwaite are offered on the TVM at Oxford Road even though there are no direct trains!)
3. Manchester Stations include Victoria, Piccadilly, Oxford Road and Deansgate, and your season will take you to any of these, unless it is 'Route Hebden Bridge', since Calder Valley services go only to Victoria.
4. Depending where your final destination is in central Manchester, you may find Salford Central a more convenient stop (change at Victoria except for one through service daily), but for flexiblity you should then book an 'Any Permitted' season for Salford Crescent, which will be valid via Victoria or Piccadilly.
5. It is not possible to book through tickets from West Yorkshire to Manchester Central Zone, but there are three free City Centre bus routes that serve Piccadilly (1,3) Victoria and Oxford Road (2) and Salford Central (2,3)
6. PM Peak Hour commuting tips; go for the xx07 from Oxford Road, and you'll almost certainly get a seat when passengers from Liverpool get off a few minutes later at Piccadilly. You also have the option of then getting off at Stalybridge (xx26) for a leisurely pint at the Buffet before catching the xx42 stopper to Huddersfield.