Originally Posted by
lethum
Avalon works if it has prana and a connection to Saber. Avalon no only healed Shirou from the worst of the Fuyuki fire damage, but it passively protected him from disease and generally worked partially.
Before Saber's around to do provide prana to Avalon directly, Shirou has the typical fast healer trait of main characters. Nothing to make people go "lol Wolverine" but enough that it could be odd for anyone who knows how the body works.
To summarize my opinion, yes, you can ignore Avalon, except for the whole fast healer thing. And the "immune to disease and probably some poisons" thing.