So...?
What is the solution?
Keep in mind our goal which is to find the best and safer way to let EM install successfully the maximum of MODs.
So in this context, full lines FIND for REPLACE WITH will drastically decrease EM chances to succeed, and WILL create (even manually and you knows it) issues for users as they will not be able to find these full lines to replaces them (you can't separate the 2 issues: you need a full line FIND before a full line REPLACE WITH).
On the other hand, IN-LINE commands are a "bit" more risky if you don't use EM. But is it really a sufficient reason?
Manual installation compatibility is preserved with the current official phpBB MOD template, this is enough no?
In fact, my real opinion is that EM will be very powerful and safe enough, so the majority of MOD installations in the future will be proceed by EM. So the "little" difficulty occurred by the necessary use of IN-LINE commands for manual installation is a minor problem IMO.
And in case EM has trouble to install a MOD, don't forget that you may uninstall it safely, immediately after having install it and done some tests (before unlocking the board for users).
Then, I really think that manual MOD installation will decrease quickly as soon as an EM final release will be available.
Just my 2c