Leaving ISIS aside, it's one of those things that are considered norm. Like, "oh, the sky's blue", "the world's still revolving", "Najib's still a d*ckhead", "Oh, Poslaju you incompetent sad excuse of a postal service..."
Just one thing though; if you purchase figures based on its expected market price, then maybe it's time to re-think why you collect in the first place? I began collecting in the first place because Tharja's awesome, and then there's Cordelia, and oh look at all these cute plastic butts... which I branch out to various figures of characters that I like. Of course I sell my figures too, but it's because either I was disappointed in the sculpt, or I no longer like the character. Not because I thought I can sell it for 200% aftermarket. It's terrible financial decision.
Even if you choose to ship when all items are in stock, that's not exactly how they do things. I got the short end of the stick with Toranoana recently, where I placed multiple separate pre-orders, but made sure to choose "予約定期便", which kinda means that instead of shipping out your goods as they are in stock, they'll send out your stuff on delivery day (which is Tuesday) once per week. This led me to believe that as my goods become available they'll just combine everything into one order and ship them out next week. Heck, it's almost common sense.
NOPE. Three pre-orders containing one single light novel each, all shipped separately ON THE SAME DAY, I got THREE different tracking nos, which also meant I had to pay 420 yen for each shipment. Oh, and that 420 yen is a flat rate, meaning it doesn't matter if you have one single thin book or 5 figures in one shipment. I just wasted 840 yen when just combining everything into one shipment would have made much more sense.
I mailed the customer service, behind all the formalities they explained that it was because I placed each order separately; if I wanted everything in one shipment I should've "placed everything in my cart first then only check out". Yeah right, and miss out on buying when the quantity is very limited in the first place?
I seriously have no idea why Japanese-run online store still cannot do mail order properly.
Actually (for HLJ) if you first send them to warehouse, you can actually delay the shipment (if they have the items ready) for 60 days. You can wait for all item you ordered to be in-stock, then only you grouped them together for shipment.
For your case, I think even Amiami did that; they will treat each individual order separately, even if the item inside each shipment is same. You need to combine the orders if you want to send them together. They cannot just unanimously combine your shipment; who knows it was intentional (to avoid custom, for example)? For Toranoana, are you able to combine your shipment using whatever user control panel you can access? If they don't provide such option, when they invoiced you, can you email them and request combination?