If you're doing this at such a scale that encoding speed matters (like if you're Instagram) the major concern would likely be cost, which you're going to save in bandwidth every time an image is viewed.
How am I going to "throw more CPU power at the problem" when I'm using a scanner hooked up to my laptop? Should I buy myself a new, more powerful laptop? That doesn't sound cheap.
As for "just" waiting... my time is valuable, and I have better things to do with it than wait... and, unfortunately, the process of scanning and encoding needs a lot of babysitting from me, so I can't just dump a bunch of photos in my scanner and come back when it's all over if I want even half-decent results, not to mention archival quality images.
In this real-world scenario, a quicker encoding speed would save me a lot of valuable time, and there's no getting around it short of hiring a skilled and trusted person to do it for me.
The use of intermediate formats is a well proven technique in video editing where encoding real time to AVC/HEVC at high quality is not possible. Codecs like ProRes are used that are much easier to encode to at the expense of storage space.