For one thing, HQ2 will never have 50,000 employees, not even 20 years from now. The Seattle office still doesn't have 50,000. I don't know how many it will ultimately be, but 50,000 was a teaser number that existed only to stimulate proposals.
For another thing, nowhere near 100% of HQ2 employees will ride the T. Many will walk from new and existing residential nearby and some will drive (from near and far).
I would be surprised if HQ2 added more than 10,000 people to trains and 5,000 to buses 20 years from now. For downtown, spread over multiple lines, that would be in the noise. For Suffolk Downs or other non-downtown location, that is a modest load for a single station and light for 2 stations. Especially easy for the 2 SD stations that already barely have any ridership.
Actually, Suffolk Downs is the least used station among the 3 heavy rail lines with only 500 boardings per day.