OP it seems very unfair that you would be effectively penalised for being on unpaid maternity leave, despite the technicality of the small BIK. The principle in most cases is that these types of leaves should not leave you worse off outside of the agreed unpaid salary - eg you accrue BH and AL during this time, and in this case your health insurance benefit continued. Are they including this accrued leave in the SCSB calculation too, as it effectively is an emolument?
I would imagine this sort of case has come up before, as a lot of large multinationals offer health insurance and BIK is of course charged. They are the companies that are paying more than the standard severance payments and probably tend to have a workforce in the childbearing years. It may not have happened in this company, which is why they are being cautious.
One thing that is unclear, how exactly did they charge the BIK, was it on return from unpaid leave as a bulk charge on your first pay? Although you had the benefit of coverage during this unpaid period, Revenue would always argue that date of payment is the relevant one for taxation - ie I pay 2025 tax on my bonus related to 2024, if I get backpay in 2025 for 2024 I pay 2025 tax on it.
I do recall in my payroll days that we often did an approximation of tax on severance payments, taking the conservative approach. If the employee had overpaid, they could reclaim it from Revenue and the company was never at risk of not withholding enough tax. In another firm I worked in, they didn't allow any tax relief on the first tranche of severances, directing employees to submit a tax return for overpaid taxes. Obviously this caused a lot of issues and eventually they changed their methods. By the time it came to me in a later tranche they had started allowing them and in my case I had nothing to reclaim as it was done by the company correctly (which I was able to validate by my payroll experience).
So what I am saying is, all is not lost even if your employer is calculating your tax reliefs this way, you can still argue your case with Revenue as they are the final agency which can confirm the correct tax reliefs and refund you if you have overpaid.
I would even go so far as to ask your employer for independent external advice on this. There may be a firm that specialises in this sort of calculation and has seen the facts of your case before and can confirm the correct outcome.