I'm not a huge fan that GL plugins can't be developed with SuiteScript 2.1 yet, but it's definitely a powerful tool. Many countries can only have taxes properly calculated in NetSuite because of GL plugins.
Since TaxJar is a bundle and assuming all the configuration is done correctly, it could be a gap on the app. For sure the best way to go is to have the tax determination app working correctly for all different scenarios, but if there are gaps it could take a long time for TaxJar to fix it. If that's the case, my recommendation would be to have a GL plugin in place supporting any scenario that is not supported by TaxJar yet.