EPP wanted indiscriminate scanning instead, not targeted one (the goal of the amendments).
A more limited bill takes off the pressure to "do something", and therefore makes the more extreme bill harder to pass later.
In this case there is reason to suspect that the real goal of the bill is not catching pedophiles. Instead it is to give police broader powers of surveillance in the name of catching pedophiles, which they will then be able to use for other purposes. This is particularly problematic given the ways that it could be abused by some of the more authoritarian governments in the EU. Yes, I'm thinking of Viktor Orbán of Hungary.
Specifically for the European Parliament, this is also why, while it is true it doesn't have the power of legislative initiative, given the ability to amend at will any "law", in practice it doesn't make much of a difference.