Money is fungible in some situations, but I think there are others where there are laws against using it the wrong way. Laws enforced by IRS agents with fines and penalties at their disposal during audit. I think that:
1. IRAs are for money earned by employment.
2. Many real estate investments are considered "passive", hence not employment, hence income from them not eligible for IRA. Your account is telling you your properties are in this category. He/she is expressing rules from the IRS about this. Violate them at your peril. If you don't like the accountant's opinion, get more details from him/her or find someone professional who is sure, but if they're right, they're right.
3. Other real estate investments are considered "active", hence self-employment, hence income from them is eligible for some types of IRA.
4. IRA is not the only option for tax sheltering retirement income, but all of the govt-sponsored accounts related to income are based on employment, not passive income. (I am differentiating these from accounts such as 529 education accounts.) In tax planning, it's really important to learn the distinction between active and passive income.
Since you already have a 401k and an employer, why not do an IRA based on your regular job, where it's clearly legal?
Here is a summary of employment-related retirement accounts for self-employment, in case you quit your job.
https://www.nerdwallet.com/blog/investing/4-retirement-plan-options-selfemployed/If I were going to look for tax breaks on real estate because my real estate produced too much taxable passive income, I'd investigate buying passive income properties from within my IRA account(s)..including IRA accounts that I created by converting my 401k to an IRA if necessary. Curious if the accountant has an opinion about that one...