I believe Amazon deeming certain items as HSA/FSA eligible is purely to allow you to directly use the HSA/FSA card. Amazon is absolutely not the authority on what does and does not qualify -- if you think an item qualifies you simply buy it with another payment method, save the receipt, and reimburse yourself from the account. I recommend doing this anyway as it allows you to take advantage of cashback credit cards. It also facilitates returns/refunds etc.

If you pay $101 for something and only have $99 in the account, you'll submit the entire expense, and be reimbursed $99. You could reimburse the remaining $2 later, if the FSA balance increases. Some FSA administrators will keep track of this for you and automatically send you a $2 check as soon as you're funded.