Yes, mods have their own "namespaces", or better said number ranges.
E.g. bigob index 654 in XCF will internally in the engine be for example 1654, same index 654 in your XCF submod will be for example 7654... depending on the position of the mod in the mod list and on the mod's reservedSpace.
You cannot manually define globally unique indices, even if you wanted to, so don't try.
The only exception are the vanilla (UFO1994 / TFTD1995) resources that are shared across mods, e.g. bigob index 15 will always just be 15 internally, never 1015 or 5015 or 19015.
Applies to the following image and sound sets: BASEBITS.PCK, BIGOBS.PCK, FLOOROB.PCK, HANDOB.PCK, HIT.PCK, INTICON.PCK, SMOKE.PCK, X1.PCK, Projectiles, UnderwaterProjectiles, GlobeMarkers, BATTLE.CAT and GEO.CAT