As you already pointed out, there are basically three aspects that will differ with using the native focus length vs cropping in.

Amount of Bokeh

If you use a wider lens, the amount of bokeh will be less given the same distance. You may compensate partly by moving closer - however you asked about cropping instead.

You can use one of the online DOF calculators to see if that could be a problem for your photography. If you want more DOF it might be even an advantage. This is why APS-C Cams are liked by some wildlife photographers: More reach and a bigger DOF.

Background Compression

If the angle of view changes, the ratio of visible background behind an object in foreground changes, especially when very near to the subject.

This is a bit tricky: if you do not move, the angle of view should not change. So in your scenario with only cropping, this should not be a point.

However, it will become one if you instead mover closer. This will be very noticeable if you use narrow paper backgrounds.

Image Quality

You already said, that the middle of the image circle is usually the sharpest part. So of course cropping in will reduce IQ a bit, but you are having a bit more room for that by using the best part of the image. I doubt that it will be visible at all under normal circumstances. So you can disregard this one, as long as you start with a halfway decent lens.

Conclusion

So you could indeed argue that a wider lens is more flexible, as you can always crop in, but never "crop out". However, it comes at a price in image quality. The amount of cropping you can get away with, depends heavily on the image quality of the lens. Plus you need to center your shots to minimize distortion. Very wide or very tall motives might be more difficult to shoot due to that.