The Bank of England inflation calculator says that £20 in 2005's money is equivalent to £36.44 in November 2022's money. Obviously the inflation that this calculator uses may be lower than the amount by which rail fares have gone up (and it is understandable that Penalty Fares should remain in some sort of proportion to rail fares), but even that doesn't come close to justifying £50, let alone £100. You could possibly argue £40 as being an inflationary increase, but no more than that.£50 isn't that much when you consider rampant inflation, it can't be far off the spending power of £20 when it was first changed to that
It hasn't been carefully designed to minimise fare evasion or revenue protection costs - it's just a remnant of Shapps' obsession with threatening people with huge "fines" (c.f. the £10k FPNs for breaking various Covid related laws at different times).