Your main idea is more or less correct. The cosine hidden in the projected solid anglearea measure $$dA^\perp = dA\cos(θ)$$$dA^\perp = dA\cos(θ)$ compensates the weakening of irradiance due to incidenincident angle (the Lambert's cosine law). This makes radiance independent from the incident angle. MiMy guess is that the main motivation was to make it more practical to work with.
The cosine in the rendering equation comes from the definition of BRDF:
$$ f_{r}\left(\omega_{i}\rightarrow\omega_{o}\right) =\frac{\mathrm{d}L_{o}\left(\omega_{o}\right)}{\mathrm{d}E\left(\omega_{i}\right)} =\frac{\mathrm{d}L_{o}\left(\omega_{o}\right)}{L_{i}\left(\omega_{i}\right)\mathrm{d}\sigma^{\bot}\left(\omega_{i}\right)} =\frac{\mathrm{d}L_{o}\left(\omega_{o}\right)}{L_{i}\left(\omega_{i}\right)\cos\theta_{i}\mathrm{d}\omega_{i}} $$
Which can be rewritten as
$$ \mathrm{d}L_{o}\left(\omega_{o}\right) =f_{r}\left(\omega_{i}\rightarrow\omega_{o}\right) L_{i}\left(\omega_{i}\right) \cos\theta_{i} \mathrm{d}\omega_{i} $$
Which can be integrated over the hemisphere the get the radiance reflected in a given direction $\omega_o$
$$ \int_\Omega f_{r}\left(\omega_{i}\rightarrow\omega_{o}\right) L_{i}\left(\omega_{i}\right) \cos\theta_{i} \mathrm{d}\omega_{i} $$
Voila, the rendering equation!
PS: Sorry aboutConclusion: Althought both cosines come from the changed notation ($\omega_{i}, \omega_{o}$ vs. $\omega^{\prime}, \omega$). I find this one more practical. I can rewrite it if it confuses yousame fundamental priciple, they serve different purposes.