I’m on vacation, so I can’t test this.
Theory: 3.5” sata shucks probably run at 250MB/s or so. Well below the sata 3 (6g) max. Sata ssd’s run much higher. Using an hba in x16/x8 with 3.5’s are still capped at the drive speed.
For the useless x1 slots, why not get an adapter to power the hba’s, run your 3.5 shucks off that. Keep your on board sata for ssd’s. Save your x16/8/4’s for whatever else (10gbe, pcie ssd’s, etc).
Is there a downside to running your server like that?