I don't see a reason why it should work in the main while shouldn't in the pdf utils operation.
Are you sure this properly resolves /lib/bootstrap/dist/css/bootstrap.css ? The same is in both result and cover when you inspect it?
Are use sure the bootstrap isn't applied? The bootstrap has different styles for printing and normal browser display. jsreport by default uses media print, so the pdf output may look differently than in the browser.
You can use Template.Chrome.MediaType prop for setting the screen media that browsers use for display.
https://github.com/jsreport/jsreport-dotnet-types/blob/master/jsreport.Types/Request/Chrome.cs#L29