Yep, it still would be the same. The patch changes have to be sent at the start of a sequence so the correct instruments are heard. Usually it isn't an issue if you are working on a song because the patches are sent first time and then remain selected so then starting somewhere later in the sequence uses those same sounds. It is only if the patches are reset that the problem would arise.

You would have to embed patch changes through the entire sequence to solve this problem.

After you have played sequence once then the correct patches are selected so I'm curious, when is this a problem for you?