Pixelmator Pro: Negative to positive inversions and layers

Yes, Pixelmator Pro supports both negative-to-positive inversions and a full layers system.

Inverting Negatives to Positives

Pixelmator Pro features a dedicated Invert tool designed to swap colors entirely, turning a photo negative into a positive image.

• How to use it: Select your image layer, then navigate to Format > Color Adjustments > Invert.
• Note: If you do not see it immediately in the side panel, click Customize at the bottom of the Color Adjustments pane and toggle Invert on. You can then use the Intensity slider to control the inversion.

Layers System

The software functions as a comprehensive, layer-based image editor. Its layer architecture includes:

• Diverse Layer Types: Support for standard image layers, vector shapes, text, and video layers.
• Adjustment Layers: You can apply non-destructive color and exposure corrections on separate layers without permanently altering your original image. 
• Masking & Blending: Offers robust layer masks, clipping masks, customizable opacity sliders, and standard blending modes (like Overlay, Multiply, and Difference)

More info from Apple: Intro to layers in Pixelmator Pro on Mac - Apple Support

If you are going to learn a new piece of photo editing software anyway, you might consider Affinity Studio. I know several photographers who recommend it highly, and as long as you have no need for the AI features it is completely free and offers the features you are looking for.

https://www.affinity.studio/get-affinity

I will note that I don't use it personally (I am an avid photographer, but my workflow is mainly DxO PhotoLab for RAW conversions with occasional editing in Photoshop CC, supplemented rarely by Nik and Topaz, and occasional niche tools like Helicon Focus for stacking).