Remember that prices are nothing to do with filling seats, they are to do with maximising revenue extracted from the passenger. One person may be willing to pay upto £40 for a journey before considering alternatives (different time, different method, not travelling), one upto £60, one upto £120, one upto £200.
If there are only 3 seats, and there are penalties for standing, the task that the TOCs have is to ensure that not just the £200 person travels, but the £120 and the £60, that raises £370 in revenue. They have to ensure the £40 doesn't, and ideally takes another train.
If they price the ticket at £200 they'll raise £200 and have 2 empty seats
If they price at £120 they'll raise £240 and have 1 empty seat
If they price at £60 they'll raise £240 and have 0 empty seats
If they price at £40 they'll raise £160 and have standing.
If they can somehow charge those individual fares, then they have 0 empty seats and £370 in revenue.
They do this by things like making Lancaster-London tickets cheaper than Preston-London, by selling advanced tickets (and indeed advanced from certain stations and not others)
If the goal of HS2 is to transport the maximum number of people, then reducing the price will increase the number of seats, even if it abstracts passengers from the road/air and from slower services.
If the goal is to make the most money (or require the least subsidy), the trains will be like the 'peak' manchester-london train I'm on now, with just 1 of the 9 seats I can see from my current seat occupied, but they'll be charging £250 each way, and those who want to pay less will take the slower WCML stopping services, meaning that any extra capacity there won't be realised.
I suspect the latter.