Does anyone have any experience of the 2nd/3rd parts of this course (level 5 & 6) - reading through the handbook, the first year modules seem very structured and focused, then the 2nd year is more critic than creative (ie. researching other people's photographs instead of making your own) - and the 3rd year is so completely vague that the two modules have virtually identical descriptions...

maybe this is normal for an Arts degree...
Hi Flossie. I'm currently working on Your Own Portfolio having gone through the full set of L1/2 courses (i.e. no APEL - TAOP, PAP, UVC, PWDP and Landscape). The three different levels are indeed very different, that's a fair comment. However, there's more to it than what you've said.
From my own perspective, Level 1(4) provides you with the basic tools and a dose of confidence to get out there and take photographs. For example, TAOP is very structured, take photographs that show this or that: looking at contrasts for the assignment is a classic example. Yes, you can take a photograph of a pin and a hammer (sharp and blunt), but if you put the time in and do some research at this early level, you can do something extra. So you see, looking at other artists is not something just for the later levels....
At level 2(5), there are still requests to take a photograph to show something in particular, but by this point it is expected that you will be more confident in achieving things, perhaps more willing to take risks with your photography, for example I photographed roundabouts to show the progression of the seasons - yes, that was a risk, and I'm hoping to soon find out whether it's paid off. There's also the more academic side of things coming in too (an essay per module), which can be a bit of a shock after the L1 stuff. However, it's an honours degree at the end of the day, and you don't get a degree just because you've read Amateur Photographer for the last 20 years (if you did I'd have one in photography, one in film and cinema, another in IT, one in football, etc. Oh, you get the idea). At this level you are still making your own photographs too, don't be fooled into thinking you don't.
I'm just at the start of Your Own Portfolio, and yes there's less structure to the notes, less direction. This is to allow you to head off in directions that interest you, or at least that's how I see it. For example, if I wanted to shoot wildlife, I could do it. There isn't a previous module on wildlife photography although you can use the genre to illustrate the subjects requested in TAOP, etc. Yes, this is quite daunting, and I admit that I feel a little dizzy from the prospect of heading forward, but that's only because I haven't decided how or what I want to do yet. Once I've gestated that idea, there's only one way forward.
Anyway, I hope that helps. I don't pop up on here very often, but if you (or anyone else) have any specific questions, give me a shout on the Flickr forum...