Yes, you've got it right, it sounds like you have a 0.29% overall expense ratio for that investment. I would say those $1 fees are an additional fee. Probably every time you transfer to the investment account or make a new purchase in the investment account. You might consider moving to Fidelity which has an excellent HSA. You'll probably want to continue to contribute to the workplace HSA for the FICA tax deduction that you're likely getting (the income tax deduction is the same either way), and then transfer it out.
There's probably a transfer fee, so instead you'll want to take a withdrawal just like you would to reimburse yourself for medical expenses and then contribute to fidelity as a rollover contribution. You're limited to doing this once per rolling 12 month period (not per calendar year), so you'll end up with a years worth of contributions sitting uninvested at the end of the year. This is what I do to avoid these kinds of fees at a workplace HSA.