My fear is that financial pressure driven by the huge cost over-runs will focus on a full blown airline style yield maximisation model.
Like LNER, you mean? I don't doubt that when that rolls out more widely they'll do stuff like remove the safeguards and potentially even suggest why the Anytime fare should either be removed or increased to four figures to give them more scope to increase the fare when busy...
(Airlines do or did technically have maximum fares - the IATA interavailable single - but it's swingeingly expensive - it makes Avanti's ridiculous London-Manchester Anytimes look cheap)
But yes, I have a massive fear that they'll stick with the 3x200m/hour Manchester service and just price it to the absolute hilt to maximise income rather than finding a way to up the capacity, be that building some 400m classic line platforms or playing with portion working to get up to 4 or 5 an hour at busy times of day.
Birmingham perhaps less so, though, as 3 x 400m is a huge amount of capacity, and there's no practical way of them pricing Chiltern up to the same extent because even if they did it with the through tickets you could just string together a split out of lower priced day returns (and I believe there's legal precedent against BR from the 1980s/90s that means splits can't be banned, unlike in the Republic of Ireland where they actually are banned). Also Birmingham-London is short enough that most people would consider driving if the train was too costly, so there's solid competition - Edinburgh/Newcastle are a bit different because it's a bit far for most to drive. Yes, driving to London is grim, but driving to somewhere like Luton Airport Parkway or an outlying Tube station is fine.