The "penalties" referred to in the article are for excess contributions that are not withdrawn before the due date of the return next year.
If the Maryland Legislature or the IRS addresses the issue to allow HSA contributions to be deductible in Maryland at some point in 2018, then all the contributions up to the limit should be allowable, because the last month rule comes into play so long as the taxpayer is still covered by an HDHP on December 1, 2018 - this rule sets the annual contribution limit to the maximum, as if the taxpayer had been in the HDHP all year.
Of course, if the taxpayer is not in an HDHP on December 1, 2018, then the month(s) in which the HSA contributions were not allowed would have to be added to the other months the taxpayer was not in the HDHP for computing the annual limit for 2018.
In any case, HSA contributions should be held up, but if one of the two agencies "fixes" the problem before December 1, 2018, then the regular amount for the year can still be eventually contributed without penalty. Alternatively, if the two agencies don't eventually fix the problem, the taxpayer can still continue to make the contributions, but know that he/she will have to withdraw those contributions as a "Mistaken Contribution" before the return's due date. In this case, there will be no deduction for the contributions, but no penalty for excess contributions, either.
