The guitar plays the same line with a synth. It was just a midi-synth in the original. I'm not sure if I would have preferred it left out.
However, I think it sounds a lot better as a whole. Seymor's theme, won't necessarily sound like the black mages versions, it depends which instruments they use and how they're played (Dynamics, ETC). The black mages are also a bit abrasive (lol).
There are going to be arguments regardless. If they didn't do anything people would complain they were lazy. i guess they could include every version of the soundtrack, that would be unprecedented as far as I'm aware.
For FFVII's PC mods there's arguments all the time on which collection is the best one (Aside from the actual PC Version which is deemed craptacular by all), the PSX version, the Soundtrack Version OGG Looped, Ones with Better instruments FFtim, and ones that are taken from Orchestral Renditions, or a mix that varies from person to person.