In Motion, how can I set some layers to loop while others stretch with the generator on a FCP timeline?

No - I was talking about building an Effect in Motion as a template *for* FCP. You can drop an Effect on just about anything — clips, stills, titles, and generators and Effects will work the same for all of them.

To make a simple progress bar, you can have a solid rectangle the width/appearance of the you want, create an outline, and animate the solid rectangle "through" the outline at an even pace. No matter how long you make the template Effect, it will animate however long the clip/other it is applied to.

When it's published, you can just drop it on your heartbeat generator — no matter how long you make it — and it will keep the animation from beginning to end just as you want it.

When you make it, you might want to add (publish) some extras, like size and color and possibly vertical positioning... stuff like that.

One of the simplest setups is:

Create the progress bar with a rectangle and add the roundness you want to the shape.

Duplicate the rectangle twice - one with a solid fill - the other just the outline.

To the original, Add an Image Mask and add the first duplicate (solid) rectangle to the Mask Source.

Move the playhead to the first frame, set the X position of the original rectangle so that it's right side just touches the left side of the mask rectangle.

Set a Keyframe.

Move the Playhead to the Last Frame (or the next to last frame) and set the original rectangle position X to 0.

Play. Publish.

For a repeating/looping animation in a Generator, I would recommend a Project Loop End marker.

My recommendation would be to make the progress bar an Effect that you can add to your Generator in FCP (as well as just about anything else in FCP except transitions).