Expand use of CheckIRId stores (#5820)

This is trying to make it clearer when vectors are being indexed with
`CheckIRId`.

The only one that I still kind of want to change is the
`SmallVector<std::unique_ptr<CompilationUnit>>`, but because it's a
`unique_ptr` that's a little more complex. I may not bother.

Note, some of the changes around nuanced `SmallVector` interactions were
based on trying to copy the way `SmallVector` itself takes arguments,
like with range passing.

toolchain/check/import_ref.cpp

@@ -64,7 +64,7 @@ auto SetSpecialImportIRs(Context& context, SemIR::ImportIR import_ir) -> void {
 
 auto AddImportIR(Context& context, SemIR::ImportIR import_ir)
     -> SemIR::ImportIRId {
-  auto& ir_id = context.check_ir_map()[import_ir.sem_ir->check_ir_id().index];
+  auto& ir_id = context.check_ir_map().Get(import_ir.sem_ir->check_ir_id());
   if (!ir_id.has_value()) {
     // Note this updates check_ir_map.
     ir_id = InternalAddImportIR(context, import_ir);