Here's a missing scene that explains a bit about why William and Carson respect Mr Bates, and why Thomas despises him.
Thomas rounded the corner and entered the butler's pantry, only to be brought up short by the sight of William and Mr Bates sitting at the table, silver polish between them, and the silver carefully stacked in three piles, one unpolished, one polished, and a final stack that was polished and cleaned, ready to be put away. The pair looked up from their work, rags in hand.
"What's this, then?" He asked William.
"This," Bates replied scornfully, "is polish. That," he pointed, "is his lordship's silver. And polishing it, one of the tasks of a footman. William has been working at it this last hour. Pity you were too busy, Thomas. We're almost finished, but you could pick up a cloth and help."
William hid a smile, while Thomas glared. Not having a reply at the ready, he pivoted and returned to the servant's hall, where Miss O'Brien was putting careful, tiny stitches into a dress that Lady Grantham had discarded. Thomas picked up the pack of cigarettes next to her, and lit one.
"Interfering bastard." He snarled.
"Who would that be?" She asked.
"Bates. He's in there, silver all around, with William. Who's he trying to impress?"
Miss O'Brien smirked. "If he's trying to get on William's good side, he's wasting his time. That boy's too dozy to have a bad side. Mr Carson won't like it, though. He doesn't like anyone near the silver, when he's not there to watch over it."
Thomas exhaled the cloud he'd been holding. "Maybe I should tell him what they've been up to."
O'Brien smiled. "Maybe you should."
Back in the butler's pantry, William was stifling a laugh, and Mr Bates had what passed for a grin on his face.
"Did you see the look on his face, Mr Bates? Thomas didn't know what to say to you."
"Well, I had a lot more time to think than he did. I knew he'd try to catch us out. When did Mr Carson say he'd be back?"
"Not for another half-hour, yet. If Thomas is still chatting with Miss O'Brien when he comes through, he'll catch it, for sure."
But when Mr Carson returned, Thomas was nowhere in sight, and the silver was all polished and cleaned, and laid out for his inspection before putting away.
That night at dinner, Thomas brought the subject up. He figured that public humiliation was a better revenge than a quiet scolding.
"Mr Carson, I noticed that the silver cabinet was open this afternoon, while you were out. I know you don't leave it unlocked it unless you are present, so I was concerned." He missed the glances that shot between William and Bates at that. Mr Carson had just taken a mouthful of Mrs Patmore's stew, and was temporarily unable to reply.
"Are you sure you want to describe what happened this afternoon, Thomas?" Bates asked.
"Yeah, Mr Bates, I am. You were in the butler's pantry, where you've no cause to be."
"And you weren't." Bates replied evenly.
"No, I wasn't. Mr Carson doesn't like us to be in there unless he's there to supervise. I don't know why William was there, he should know better."
Mr Carson swallowed, and put his silverware down on his plate, always a signal that he was preparing a scold. Thomas tried to angle himself to look respectfully at Mr Carson, while not missing Mr Bates' chagrin at being the recipient of one of Mr Carson's set downs.
"This afternoon, Mr Bates was good enough to stand in my stead for a couple of hours, while I was called away. His Lordship needed my presence at a meeting with the wine merchants. I unlocked the cabinet, and Mr Bates promised to remain in the room the entire time that William and you were polishing. When I returned, the silver was polished, and I had no idea until this moment that you failed to assist William. It is your responsibility to polish the silver every Wednesday afternoon. What made you think that today was some sort of holiday?" He glared at Thomas.
"Well, but you weren't there- "
"Thomas, the tasks assigned to you are always there, and I would hope that you perform them whether I am watching you or not. My leaving the premises does not translate into an afternoon off for you."
"No, Mr Carson. But you never leave the cabinet unlocked unless you're in the room."
"It's true that I don't normally do so, but that is because in the past, there has not been a senior enough member of the male staff that was willing to help. Mr Bates heard that I was busy this afternoon, and generously offered his time. As we have all heard that his lordship trusted his life to Mr Bates, I decided that he could also be trusted with his lordship's silver. It now appears that he supervised William and performed your portion of the work as well. Perhaps you could tell us just what you were doing this afternoon?"
"Well, -" Thomas stalled, trying to think of a good enough excuse.
"Mr Bates, when you saw Thomas, did you ask him to help William?"
"I did, Mr Carson. He seemed to be too busy, but he didn't mention just what he was doing."
"To clarify, Thomas, when a senior member of the staff makes a request, in the future, you would be well served to respect it. And I would like to thank you again, Mr Bates, for your assistance this afternoon."
"You're welcome, Mr Carson." Mr Bates bit his tongue to keep from making any further remarks. He did glance across at William, who was biting his cheek so as not to burst out laughing, and took in Miss O'Brien's sour look at the same time.
"It was very kind of you to help, Mr Bates." Mrs Hughes added.
"It was nothing. I enjoyed myself."
Now Anna was smiling, as well, and he didn't know how he could contain his own grin, but he managed, barely.
As the valet's job does not seem to be very taxing, I expect that Bates found things to do in any part of the house that allowed it. Peeling potatoes for Mrs Patmore? Dusting with Anna and Gwen?