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I do not know that transmission. But it looks like the number 2 picture shows a case bolt, not for adding or draining.

What you need is a good parts book photo with parts descriptions.

Yes, I wasn't sure if it was a case bolt. It was just that it's the same place a some of the drain bolts I've seen. So weird. I can't see any other bolts on that side.

So far I can't find ant parts book images for non-Auto or diesel.

 

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So the mystery has slightly cleared.
After finding a forum post that suggested searching for Civic fluid change videos and linked to this one

I've crawled back under my 2007 manual crv and located those same bolts. They are wet from a dose of WD40 btw.
They are. 11 and 17 on the diagram below, and both have crush washers fitted.

Now my final issue question, is do I go ahead and fill it like they do in the video, through the higher plug in that photo, until it starts to drip (like doing the rear diff). Or do I go back up and remove the batter box to access what seems to also be a fill point? It is mentioned in this diagram, which is of my actual model, as a plug (17).
I'd rather do it as seen in the video as it is less hassle. Any reason not to?

 

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Personally if I have a drip hole, I go that route to check the fill level. As far as getting the fluid in, my 08 CRV uses the dip stick tube, my 2011 Pilot used a huge fill port on top of the tranny and a drip level check and my 2019 Ridgeline and 2016 Accord use the dip stick. These take longer to get the fluid in and you have to wait till it drains in to the transmission. Level checking often takes several minutes and four or five checks.

One caution on using the drip /fill port and draining it is that you want to crack the fill plug loose first and leave it in place. Then pull the drain plug. Don't remove the fill plug until the flow has slowed way down else you will shoot transmission fluid across the garage. Ask me how I know.

So the 2007 mk3 manual petrol I have doesn't have a dip stick for the transmission fluid. That mainly seems to be on the AT and diesel ones. It seems like every single iteration had a different set up which is annoying.

Good tip about waiting to remove the fill plug, I would have whipped it straight out.

What seems to be an actual fill port is a bugger to get to as you have to remove the battery and its cradle, along with moving some pipes. It's a hole about the size of a 10p coin and you can see the toothed cogs inside.

I'm presuming it's fine to fill the oil through that top plug pictured though right? It's going into the right place, easier to get to, and will start to drip when full.