Maths, I agree with your first response. Section 42(2) states "Subject to subsections (3) and (3A) below, where notice has been given under section 8, 8A or 12AA of this Act, a claim shall not at any time be made otherwise than by being included in a return under that section if it could, at that or any subsequent time, be made by being so included."
In my opinion, this subsection is mainly for HMRC's benefit. In short, if you can include your claim in a return either by delaying/bringing forward the claim or the return (within time limits), then do so. It is far easier for HMRC to deal with everything within one document. Standalone claims are burdensome for HMRC.
Section 43 simply sets the default time limit, recognising that another part of the legislation might set a longer or shorter time limit.
Returning to the original post:
If this is the case, does this mean that section 43 (time limit for making claims, typically 4 years) only can apply to claims which cannot be made in the tax return?
The answer is "no".