The easiest answer is something I alluded to earlier with my gaming discussion. It's not how we envision our scifi ships, but you really need engines at both ends ( some of the ships at the beginning of Nexus TJI had such a setup ). Engines with equivalent power, at that. You're going to spend the same amount of time accelerating in the forward and reverse direction.
Which realistically means that, were you capable of achieving near c velocities ( and beyond? ) you'd spend most of your time accelerating which means burning fuel, which of course lends to yet another problem. Your actual trip time would also change for the worse as well, since you would only spend a fraction of it at potential relativistic ( and beyond? ) speeds.
I forget where exactly the 'flip end for end' idea came from, but it was essentially the 'accepted answer' for having your ship's engines only on one end of the ship while still satisfying the laws of motion. However, the stresses that you would impose on the ship's hull doing so makes it a bad idea anyway.
Too bad Lagrangian points don't actually open portals to FTL travel, eh? Then all we'd need is an LDS / cruising drive.
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