Definitely get that battery charged up before setting it aside or leaving it in place and disconnected. It already lost some of its life by going all the way down to 1.6V, and will lose even more if it spends a lot of time at that low voltage.

As far as the car itself goes (vs. the battery), it should be happy with either a charged 12+V battery, or with no battery at all. In between is not so good. A charger with no battery installed could cause problems. Each time you connect or disconnect the battery to the car, there is the chance for a voltage spike causing issues. On most cars, a trick is to turn the parking lights on to dampen any spike, but I'm not sure if the BMW LCM wizardry gets in the middle of that for these cars.

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2001 X5 3.0i, 203k miles, AT, owned since 2014