I noticed Fleet uses a custom resource named "Bundle" which is the same name as Trust Manager's custom resource for CA cert bundles. Is it a non-issue because they use different APIs or is it a collision that prevents installing both CRDs?

Shouldn't be an issue-- if you need to list out the resources, however, you might need to use the full API name for the resource for one or both when using something like

kubectl get ...

but it should be able ot distinguish without issue on full API name.