Is it possible to view multiple payments on a registration as separate Contributions?
I can understand what you are trying to do - yes this is the way Civi works

For Accountant Point of View 
I guess they will be more interested in the CSV from batch export which will make more sense to them 


where you can see Credit account type clearly says 

INC (Invoice)        - 1000 
AR  (Amount received)- 10 + 990 => 1000

with different nominal codes 

If you are not happy with this output then you need to create an extension for each changes - I guess this helps