Hi Robert - in our organization we do have a 5-year Budget Plan and previously rolled out a 3-year Multi Year Forecasting.
On our Forecasting, we used 3 Labor GL Accounts to allocate the Labor costs per Cost Center using "Percentage of Base Compensation". The dollar amount is is determined by number of Headcount x Annual base compensation x Percentage. We did not use any "Flat rate" in this model.
Come 2020 Budget (which we created a 5 year plan 'till 2024), we changed our allocation rules and we are currently using 15 Labor GL Accounts. The determination of percentages and respective accounts were based from the trending analysis from YTD information.

We have also leveraged the Adjustment % column in Labor to effect any inflation rate (in our case applied 2.5%) year over year.
Just as you mentioned, since there would be some changes due to Employee increases, different bi-weekly paydays, bonuses, etc, coming from Corporate (HR), we have to consider it and make sure we account those in our Plan.
Right now, we plan to input those in IT Planning by manually entering those amounts (month over month) before we finally close the budget plan. That said, it will normalized the Monthly spend (embedding all the factors mentioned above) that we have for Labor since using the % of base compensation- approach will only allocate the $$ evenly through 12 months.
Another approach that I can think of (in your case since you are using a Flat Rate - approach) is that, you can consider using the "Adjust Amount" feature where you can define the % or Absolute amount of adjustment. You can also manipulate the Period range as determination on when will that adjustment take effect and when it will end.

Hope this somehow helps.
Thanks,
Rose