Everything you're talking about is scoped by the L2 VLAN. When servers communicate with the router or other servers, they will be doing so with packets/frames that will only be seen in the VLAN that they're sent on. The only way packets/frames can cross from the original VLAN to a different VLAN is via the router.
From the router's perspective, all the data mentioned with be tagged with the appropriate VLAN tag. The switch is adding the tag to the data from your servers depending on the VLAN assignment on the port. Since the router is Router-on-a-stick (802.1q trunk), it has to be able to differentiate traffic between different VLANs. The only way it can do that is with the VLAN tag that was added by the switch. Any responses are also tagged with the appropriate VLAN tag before sending across the trunk back to the switch.