The salary structure is very flexible. BUT people are different and grow differently.
So to expect we can do a cattle class salary structure that can apply to an entire department is expecting too much of the software. Example : 100 Freshers joining on exactly same salary and growing annually at the same rate → very rare.
Your most flexible and future proof salary structure is
1 salary structure = 1 employee. 
This is of course possible, but I think ERPNext does an ok job of finding a middle ground between total flexibility and loads of data maintenance. With a customized “salary structure employee” you can add benefits, allowances and deductions until your heart id content, but then for each employee you just have to decide if they warrant an allowance and its value for them.
Hi @mafrica,
Did you move forward with this? We can help you if you need to get healthcare work in Tanzania.
Thanks for getting in touch. I am afraid I have now moved on and no longer involved.
paul