Yes, but this is not a normal scenario, for the following reasons:
a) no club will ever do that; however, Bolton are in an almost unique position in this respect, because they will probably have significant (i.e. abnormal) transfer funds available in January compared with what any given lower league club usually has. That means the playing field is not level prior to and post the January transfer window, and by a significant margin. Luke is exactly right.
b) No club will ever do this either, so it is irrelevant.
a) No club will sign a few good players in January???? Clubs regularly sign 5 or 6 players in January!! Especially when they're in a relegation battle. And what if a club gets bought between September and December by a rich owner who pumps money in. Imagine we get the rich investor we're looking for in October and he triples our budget in time for January. Which would give us abnormal transfer funds for a lower league club. Is this suddenly unfair on everyone else in the league and we shouldn't be allowed to play? No, of course not.
b) No club will be forced to sell their best players in January? Ever? And play a team with a lot of changes post January? Ok. This is what some people think Bury, Bolton, Birmingham etc. should have been forced to do last season when they realised their were money problems. It happens.
Bolton won't be allowed to, for example, sign Andrade for £2mil in October and play him in October. Just like any other club. They wait until January before he could play.
Bolton won't be allowed to loan players outside of the window and play them. They'll have to wait until the player can be registered. Just like any other club.
Bolton will be allowed to sign free agents just like any other club at these times.
Football isn't a level playing field! Just think, Accrington got to play us whilst Bolger was s******g himself. Hopefully he's better for Rotherham. Is that unfair on Rotherham? No it's just luck. That's football not being a level playing field week to week, never mind when teams can sign different players.
In this Bolton case, we're just on the wrong side of luck because we play them later on. We'll just have to prove that we have the better team no matter who they put out by playing to the best of our abilities and winning.
(Also, weren't Portsmouth in a similar situation just a couple of seasons ago? Perhaps this Bolton case isn't as unique as you think.)