Am not sure but would suspect the 3,000 ft amsl refers to the general TA outside CAS in the UK - if operating below a TMA the TA is appropriate to the controlling aerodrome
Even if it was, the rules as written don't exempt IFR below 3000' anyway (it looks like someone vaguely intended them to, but didn't actually write it properly to do so)...
As such you have a problem if flying Eastbound, with an MSA of say 1500', and CAS starting at 2500' - the only valid levels you have are 1000' (below MSA so no good) or 3000' (inside CAS so no good), so to fly IFR in that area Eastbound is not possible (Westbound fine as you can do 2000'). If it's the LTMA above then you're never going to get a transit, so you're a bit stuffed!
Obviously there's a question of what the rules say and what people actually do...