> Will the inactivity timeout set for the application "TCP-ALL" of 900 trump the default value of 1800 for junos-ssh if the application-set were matched in a security policy?
Assuming you had both applications are configured in the same security policy, yes order matters (see below).
> Does it matter if the order of the applications in this application set were reversed?
Yes, the applications (for the same security policy) will be checked in order, from top to bottom. Juniper doesn't recommend that applications be configured this way, you could just use the default or a wildcard to say "then everything else".