"But, unfortunately, Retool’s modules do have some runtime issues and are generally not yet performant enough to be truly useful in all cases. That’s why generally, we would avoid using modules where possible."
Modules are hotly debated topic - use of them is sometimes necessary, especially in enterprise deployments and they do "the job" but come at a cost of performance, dev time and amount of tweaking required.
There is no native way of controlling rendering, tweaking modules but more of passing variables to enable/disable loading per certain criteria. Many users tend to skip this step so performance degrades with heavy use of modules.
Overall if you know what you're doing they should suffice, but there are nuances with adding/deprecating inputs/outputs that get complicated over time or stay within code causing bloat.
Also, when jumping between apps in a multi setup what are your thoughts about the initial rendering of each app (side, top, and body), doesnt this break the ux flow for users?
Regarding switching between apps there is a open bug report which is a recent change as it shouldn't be the native behavior.
These performance improvements should give you general direction and will change on the situation, need of the organization.