[Testing] Add test coverage for configuration loading

[kpollich]

In #3328, we discovered an issue with Fleet Server's configuration reloading, specifically around the APM config:

fleet-server/internal/pkg/server/agent.go

Lines 424 to 442 in 528e4ae

	if expAPMCFG := expInput.APMConfig; expAPMCFG != nil {
	instrumentationCfg, err := apmConfigToInstrumentation(expAPMCFG)
	if err != nil {
	zerolog.Ctx(ctx).Warn().Err(err).Msg("Unable to parse expected APM config as instrumentation config")
	} else {
	obj := map[string]interface{}{
	"inputs": []interface{}{map[string]interface{}{
	"server": map[string]interface{}{
	"instrumentation": instrumentationCfg,
	},
	},
	}}
	err = cfgData.Merge(obj, config.DefaultOptions...)
	if err != nil {
	zerolog.Ctx(ctx).Warn().Err(err).Msg("Failed to merge APM config into cfgData")
	}
	}
	}

Related PR: #3277

We should add some integration test coverage for different types of configuration to ensure Fleet Server loads all configurations as expected.