A lot of it has to do with PC-NPC intereactions. The same Seal jutsu that reduces your Chakra pool and attacks also dampens the amount of chakra an NPC percieves you to actually have.
So, you could have some of your chakra sealed, making the NPC underestimate you, and half-way through the fight you break the seal, removing the penalties you were taking, and take the NPC by suprise.
An alternate use is for when a sensei spars with his/her student(s), that sensei can use it to reduce his/her chakra levels and combat abilities so that the sensei doesn't just over-run the students right from the get-go.