So why didn't they include that in the HD Collection and why was 1 PS exclusive as a digital code
Nintendo paid a problematic Canadian company to make it, so it's always been a Nintendo Gamecube exclusive.
That problematic Canadian company made some flops afterwards, sued Epic Games(Unreal Engine/Gears of War/Fortnite dudes) for "providing a shitty game engine", Epic Games countersued them saying they illegally used Unreal Engine tech in their products. Epic won the counter-suit five years after and the Canadians were ordered to nuke/recall/destroy all copies of their games with stolen Unreal Engine tech that were still in the retail pipeline. They went bankrupt a year or two after that.
Japanese games fell out of favor for a while so Konami pivoted to mobile games and Japanese gyms/pinball gambling machines.
They also had a pretty public falling out with Kojima-san with Metal Gear 5.
So basically it would take too much trouble to untangle all
that bullshit.
But Sony is desperate for exclusives so I wouldn't be surprised if they hire the guys who remastered Darks Souls and Shadow of the Colossus to remake the PS1 version of MGS in a few years.