The only way in which part 142 will hurt you is in having a lower total time since time in FTDs doesn't count as flight time. Having instructed both part 141 and part 142, I think part 142 if can be better if you have a good instructor. The sim allows a lot of flexibility that the airplane does not, and it can be to your advantage if your instructor knows how to utilize it properly.

For example, the FTD is really valuable for emergency procedures and some aspects of decision making. I'd be insane to give you an engine failure at rotation in a Seminole, but I can do it in the Seminole FTD and see how you handle the situation. I had several students who had briefed that they would land if runway was available and gear down, but when I failed the engine, they struggled to gain altitude trying to fly even though they had 5,000 feet of runway in front of them. As an instructor, I could run through a lot of system failures and other bizzare scenarios which were impossible to duplicate in the airplane. Instead of asking you how you would handle a given situation, I could put you in that situation and watch what you do.

The worst aspects I saw of 142 were radio procedures and situational awareness. By the time you have a CFI these shouldn't be problems for you.