Good Intermediate Format for Combining Videos
What you wish to do is somewhat convoluted. There is a path to achieving it in the 2 step process you propose, but I would just suggest creating a new folder where you copy all the input files and rename to form a continuous sequence.

Let's say you have 3 folders and the following files in them to be joined in that order

Folder A: a001.png, a002.png, a003.png, ...... a175.png

Folder B: b0001.png, b0002.png, b0003.png, ...... b1075.png

Folder C: c01.png, c02.png, c03.png, ...... c75.png

Also let's say you want to hold the last frame of B for 5 seconds

So, you rename a001-a175 to s0001-s0175; rename b0001-b1075 to s0176-1250; duplicate s1250 120 times (24fps x 5) and rename the copies s1251-s1370, and finally rename c01-c75 to s1371-s1445.

This method avoids issues of video generation loss. For audio, WAVE files of the correct length and order can be appended losslessy by FFmpeg and then converted+muxed with the output video.

Of course, I see from your history that you have access to Premiere Pro. The simplest way of all would be to load all PNGs and audio in the editor, assemble and take output.