It's a complete non-story really. Engineering works have to be done at some point and have to be planned long in advance. Commuters are the biggest single source of income to the railway, so they have to be done at the weekend. FA Cup games aren't planned long in advance. Someone's got to pick up the short straw.
A decent indicator of the FA's own view on the matter is that the FA Cup Final has been moved to 5.30pm on a Saturday evening for the last few years whoever is playing. The FA Cup Final is the one game which can be shown live at 3pm on a Saturday during the season. Apparently the later kick-off popular with their stakeholders, whoever they are. Given the games can go on to extra time and penalties, taking around 3 hours, good luck getting anywhere up north by train after the game.
If you live a distance from the WCML or ECML then using the train can be challenging anyway. As an Exeter City fan who does travel all over the country by train to watch City, I accept there are certain times where it simply isn't practical to use the train. For instance, it isn't possible to get back to Exeter from Grimsby/Cleethorpes the same day after this weekend's game - and that's a Saturday 3pm kick-off without any engineering works. Plenty of other games would throw up problems if there were any engineering works planned - but they've got to be done at some time or other. Exeter is also better connected than many places a long distance from the WCML or ECML. Higher up the leagues, Bournemouth v Burnley or Blackburn v Swansea would present serious logistical challenges with engineering works at 3pm on a Saturday.
Like it or not, hordes of last-minute leisure travellers (given TV companies only pick games a certain number of weeks aren't a huge source of income to the railway and it isn't going to bend over backwards to accommodate them. The vast majority of away fans drive or use coaches anyway. I see plenty of away fans on my journeys going to different games, but nothing like the numbers if the train was the majority option.