Southern are actually losing a platform permanently by the end of the development. So this is likely to not only continue throughout development but beyond this date. Queueing outside London Bridge will be a permanent fixture.
They won't tell you that though. They just tell you how awesome thameslink will be.
The platforms should have far more space when the escalators and underground ticket Hall are complete but that's years away.
Then you also have the Gatwick Express which takes priority over every train on the network. So when you already have limited track and platforms, they have to freeze all trains to let the Gatwick Express come through unhindered. Doesn't matter if it delays everyone else by 5-10 minutes. The Gatwick express has to arrive on time otherwise the airport lobby will kick up a fuss.