Just to make things clear: the template modification system is being moved to debug only in the next release (consistent with other similar features). It is primarily designed for add-on developers or for advanced usage (as it generally requires detailed knowledge of technical things or some inner workings of XF). For all "normal" usage, templates should be edited directly and updated with merging. This eliminates things like learning regular expressions or doing fragile exact match replacements. 3-way merging should be much more accurate. If you use modifications, you still need to be very methodical to ensure that your changes are still being applied the correct number of times and that the changes are still valid/correct.
If you prefer to use template modifications, obviously that's your prerogative but it's not the recommended/encouraged way.