Ultimately, if your CPA is shutting you down on this, without presenting alternative options, it may be time for an upgrade. 

My wife and I were in the same situation end of 2022 where we were looking to acquire our first rental but also wanted to upgrade the primary residence. 

I'm looking to sink some money into the kitchens and bathrooms to upgrade and wanted to see if anyone can recommend a reliable crew of contractors you've worked with who can meet me that weekend to go over the scope of the project for an estimate.

Most new construction ADU projects will need a panel upgrade, potentially a conduit upgrade and right of way work depending on your utility setup.

Or buying a large house with enough restrooms where you can put dividers up to separate the space and/or upgrading the garage to an ADU. 

2) How do you balance upgrades/cap ex to protect investment versus over-investing, because it is not your forever home?

If you're looking for long-term, We have investors from literally all over the country buying these new builds.Horton has been offering all sorts of $$ towards rate buy downs, upgrades, closing costs for months and its definitely hurt re-sells.

I assume you would simply take the difference in rent price / the cost of those upgrades to determine if the return to do it makes sense?

At that point, start stabilizing the properties, proactively spend some cash on big ticket items (roof, furnace etc. that you know are coming due) or upgrades, then start paying them off.

In order to use “primary home” financing repeatedly, the new purchases would have to make sense and be upgrades from the existing duplex.