The R&D tax credit is different from the deductibility of R&D expenses under Sec. 174. The deductibility of those expenses is what's at issue here. They were previously deductible, but are no longer deductible as of January 1st 2022, regardless of whether the taxpayer chooses to take the R&D tax credit or not. This is a change passed by Congress as part of the 2017 TCJA that went into effect in 2022. It is not the IRS's decision, though it is my understanding that they have some rule making authority about the specifics of the implementation.

Because of this, you are incorrect that the two scenarios you outline compute the same as of 2022. You are correct that they did compute the same before 2022, but they compute very differently now. Scenario 2 now requires that the software business amortize any costs associated with developing new software (engineer salaries, etc.) over 5 years, rather than deducting them in the same year they are spent. This increases the business's immediate tax liability while it develops the software, and also increases its tax liability in any other years that it creates new (and probably also improved) software.