Your HSA provider is correct. No part of the $1,000 is an excess contribution because it was permitted under the last-month rule as a contribution for 2018. However, because you will not complete the testing period for the last-month rule, you will be subject to a 10% ($43) extra tax on your 2019 tax return on the $425 you would not have been eligible to contribute for 2018 were it not for the last-month rule. Because this $425 is NOT an excess contribution, it is not eligible to be returned as an excess contribution to avoid the extra tax on your 2019 tax return (and even if it was an excess contribution eligible to be returned, the deadline for doing so has passed). You are simply subject to the extra tax on your 2019 tax return and that will be the end of it. TurboTax handles reporting this extra tax.
