Yes, we could package them back into trays for larger orders (100+, maybe even 50 or less). Not a problem. In fact, we've save the trays, in anticipation we'll need to do this.
Most people buy just a few, or 5 or 10, so we package them up individually and in 5-packs to be able to ship orders quickly. PJRC strives to ship every order on the same day, if placed before the cut-off time for each carrier (postal is usually around noon, UPS around 3:30pm, USA Pacific time zone).
I think the big question is is how many can pjrc actually supply.
Our goal is to maintain a stock of at least 500 of each chip, so we can ship all small and modestly sized orders same-day. We keep about 25 to 50 on the shelf, programmed and packaged up, ready to ship at a moment's notice. The rest of kept in the original Novoton packaging, unprogrammed. The programming goes pretty quickly, so even 100 might be able to ship same day, but planning on a 1-day lead time would be wise.
I believe at this moment we're well above the 500 goal on the TQFP and 4mm QFN. I just looked and found only about 100 of the 5mm QFN. Robin says there should be more, but I didn't go digging deep (Robin & Erin don't like it when I meddle too much in this stuff). I believe we've only ever shipped just 1 order on the 5mm QFN, to a customer who bought some of all 3 types. The TQFP is by far the most popular.
1000 or more isn't a problem, but of course that's over our stock of blank chips, so there'll be a lead time. We have lots of the 4mm QFN scheduled, since that's what's used on Teensy, so odds are good we could get those faster. In a worst case, plan on Nuvoton having a 12+ week lead time to supply us with the blank chips.
If you're really going to buy a lot of these chips, we'll work with you. We're good like that. I put a lot of work in every day to help people make their projects a success, regardless of whether they're non-commerical or for-profit. We of course want to sell you a product too.
But at the same time, I need to explain something. I get a *LOT* of questions about this chip, from people who are looking to turn their project (or mere idea for a project) into a profitable product. Those questions are incredibly time consuming, especially over the phone. They're unlike technical questions, where a bug gets fixed or part replaced and the problem is conclusively solved. We've had many lengthy phone calls and many email exchanges, which you'd think should be quick and easy, since we stock these parts and we can easily get as many more as may be needed. Problem solved, right? It's rarely that simple. Really, I can identify. I spend endless hours obsessing about every new product PJRC makes, or might create. There's a lot of uncertainty, and a lot of opportunity, and a lot of excitement, and a lot of concern or worry about making a wrong decision.... like whether PJRC can really supply the chip.
PJRC was founded in 2000, and the old 8051 board was sold for years prior in small quantities (from the days before Atmel sold AVR chips). We may not be able to make a nice looking website, but as you can see from the fact the Teensy is almost always in stock, we are actually quite good at managing inventory, forecasting sales and generally running the business. You can depend upon us.