In recent discussion with Magento team front end developers they explained that Bundle is used to optimize loading of dynamic required scripts that use Require.js. And merge option is used to speed up loading of old way embedded scripts. When both Magento 2 Bundle and Merge modes are enabled it can lead to unstable work and decrease effect of each separate mode. In future they are going to restrict enabling of both conflicted modes same time so it is advised not to use them together.
It is not recommended to turn all of the JS tweaks at once. As some of them are targeted to different aspects of optimization enabling both can bring in instability and decrease of performance instead of performance increase. This is about Merge and Bundle mode. Discussed with Magento developers they share that enabling of this options same time will be deprecated and disabled in future. So you need to consider enabling Merge or Bundle mode not both of them at once.