The stock header is junk and the mod didn't make a noticeable difference to me with the 2.5R and stock pipe. The mod of cutting the header was to make it less likely to bang into the pipe when you land on your rear shock tower. When the pipe would slide into the coupler and hit the header, it would break the header every time. Or at least bend it.
The stock header breaks very easy and they are $20 a piece. I'd stick with the header that comes with the 18TM and don't modify it, just use it. It's a much better quality header and it uses a spring to hold it onto the engine. In an impact, the spring will give enough to not damage the header. Well, within reason, but it works well.
I noticed some improvement by drilling the stinger out though. Not a lot, but a little extra in the low end.