It depends on the pool.  Some (most?) pools track validity of shares on each chain separately.  I know on Bitminter for example after an LP due to NMC block change the share is still valid for BTC purposes (but not NMC).

A pool could handle multiple chains in three ways
a) only given credit for a share if it is valid for all chains
b) given credit if it is valid for master chain (BTC)
c) track each chain separately and give credit is it is a valid share for that chain (each chain has separate share count).

Slush uses method B.  Bitminter uses method C.  You are correct if the pool uses method A then there is no value in submit-stale option.