As you have discovered, it does not matter how the HSA contributions were made (through the employer or directly) and it does not matter why the distributions (spending) were made, in 99.9% of the cases, the HSA custodian owes the account owner the 1099-SA to report the distributions.
There are rare exceptions, like when the HSA custodian removes a little money from the HSA to cover service fees (the IRS does not consider this a "distribution", so no 1099-SA), but I might investigate a different HSA custodian, to find one more on top of the rules.
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