Plugin Bypass details
In each channelstrip, you will find a list of the plugins applied to that channel. Each plugin has a green button which indicates it's on/off ( or "enable/bypass") state. Mixbus's plugin bypass is a "hard" bypass. When a plugin is bypassed, it is completely prevented from processing (thus saving CPU usage). However, this means that the dry signal is not necessarily synced with the wet (processed) signal.
In practice, this is rarely an issue because most plugins (eqs, compressors) have very little latency, and those that do ( IR reverbs ) are very forgiving of a latency offset. However there are some plugins that provide a "look-ahead" delay, or other features that incur latency. For example, hardware-accelerated plugins like UAD incur a sizable delay because they transfer data across the PCI bus to the card, and back.
In these cases, you might notice a significant timing offset when you bypass the plugin. Mixbus calculates the latency offset when the playhead is "stopped". So if you want to use the plugins' hard-bypass, you should start & stop the transport each time to guarantee latency-compensation is maintained.
When auditioning a plugin in&out, it is best to use the plugin's internal "bypass", if one is provided, as the plugin developer has likely implemented a method to cleanly toggle the plugin in&out, click-free. Only the plugin developer knows how their plugin should be cleanly bypassed.