Hello, as you mentioned you might need LoRa / 4G or another communication module together with GPS, once the balloon blew up and fall down, you'll need to find your setup so you'll need GPS. the Core device has many sensors which are very useful pre-built such as gyro and accelerometer which you might find very useful (also SD card to log the data) I would suggest going with Core / Core2 device and one of the COM.X modules.
Regarding the batteries, you are right. those are LiPo batteries and they don't do well in cold temperatures, you might need to find another solution for them to replace them with. in general, I think Core will be perfect for you due to the communication module but if you'd like to tincker a bit and connect things more manually, you could go with Stick-C or ATOM device as you mentioned.