Yeah, because of #2 I don't really use containers any more. You can force dwarfs to "tidy up" by dumping the contents of bags and then reclaiming them, but that's a huge PITA. My solution is simply to keep very small inventories. At the beginning of the game, making bags is a bit of a priority, so embarking with a lot of thread, or a couple of llamas is useful (IIRC, a llama, when sheared, gives you 13 thread. Embarked llamas are ready to be sheared, so this is an economical way of embarking with a reasonable amount of thread). But your use of bags hits a steady state pretty quickly. As your grower gains in skill, you get bigger stacks of plants which gives you bigger stacks of dye, for example.
The most useful way (IMHO) is to sit down and think about how much inventory you actually need. How many cloth per month are you going to need? Plants take about a month to mature [1], so you only need 1 month of inventory. You need 1 bag per stack of plants. If your stack averages about 4 plants, and you need 28 cloth per month, then you need 7 bags for the dye, 7 inventory tiles for the bags and 7 farm plot tiles for the dimple cups (dimple cups can be grown in every season). That would allow you to fulfil a clothing job almost every day (which is quite a lot). To generate the cloth, you will need 14 farm plot tiles for the pig tails (because they can only be grown in 2 seasons), and 14 storage tiles -- you want to process them on demand because the thread/cloth doesn't stack. You need a few tiles for seeds and empty bags, so let's say a grand total of 60 tiles -- including the farm. A 6X10 room to sustain a clothing job every day doesn't seem unreasonable to me.
I think where people tend to go wrong is by building a 6x10 farm plot and accumulating hundreds/thousands of plants. Then it becomes a big problem to figure out what to do with it all. Much better to spend a few minutes planning what you will need.
[1] - This is a lie. Some crops take 25 days while others take about 40 days, but since the stack size is variable, it comes out in the wash.