One of the charms of SPFx Extensions is that they apply tenant-wide: they can be configured for immediate utilization in all modern site collections in your tenant. On SharePoint foundational level this works via the concept of good-old CustomAction that is injected into the context of each modern site collection. In the SPFx Extension package the CustomAction is configured as Feature deployment. Via the parameter 'skipFeatureDeployment' in the package-solution.json (see 'Tenant-scoped solution deployment for SharePoint Framework solutions') you can configure the SPFx Extension to be immediate available across all the sites in the tenant when the solution package is installed to the tenant app catalog, without need to explicit activate the CustomAction feature in each individual site.
This works out fine on the initial deployment of your SPFx extension: the deployed SPFx header automatically is included and active on each site.
On initial deploy, SPFx Extension included once in each modern site
However, in case of need for redeployment, you must be aware of a current glitch: the SPFx Extension gets multiplied per each re-deployment. The cause of this is in how the (semi)immediate and tenant-wide application of the CustomAction is applied. The CustomAction is not injected in the scope of each individual site (Web.UserCustomActions does not include the CustomAction of the SPFx Extension); but is injected as Tenant Wide Extensions. In case of "skipFeatureDeployment": true in the package-solution.json file, on upload / install of the .sppkg file in the tenant App Catalog the administrator is asked to set the 'Make this solution available to all sites in the organization' checkbox. If set, a row is added in the list 'Tenant Wide Extensions' in the App Catalog site. And on re-upload / redeploy, the checked setting is applied again, resulting in duplicate entries for the same SPFx Extension in the Tenant Wide Extensions list. This results that the CustomAction is applied multiple times per each site, and therefore that the SPFx Extension is included multiple times in each site...
As side-effect of re-deploy, SPFx Extension is multiplied in 'Tenant Wide Extensions' list
Result is that the SPFx Extension is included multiple times per each site
Correcting this faulty situation is simple once you know how-to (thanks to Vesa Vujonen for fast response on support question raised): just remove the duplicate entries from the Tenant Wide Extensions list. Mind you, it can take some elapse time before the effect of this is structural applied accross all the WFE's involved in serving the sites of one's tenant.
Fix by removing the duplicate rows in Tenant Wide Extensions
Then the SPFx Extension again included once, and referring to latest package version