The firing rate and damage of the weapons can indeed be globally tweaked in the final version only.
It has some settings in the Mod menu (like headshot damage), but nothing beyond that in the current version.
As for the Flak replacement, it's not possible to define the exact number of replacements in the current version, you can do something else instead:
if you open NWConfig.ini, find the [NWCoreV3.NWMainReplacer] section, and then the line starting with WeaponItemSettings[10].
From there, you can set the property bKeepItem to True of that line, as that will say to the replacer that the weapon to replace will be kept in some way.
That way, it's decided by the property MultiBehaviour in the same line, and the posssible values are:
RMT_Sequencial - Cycle between weapons sequencially (in another words, if someone picks up the Flak, then the next spawn will be The Miner, and once someone picks up The Miner, the next spawn is the Flak)
RMT_RandomStatic - Make the replacement random, which means that the mutator will decide if it should replace the weapon or not randomly
RMT_RandomTimed - Similar to RMT_Sequencial, but instead of being a fixed pattern, it's random (so the next spawn is never fixed, it can be any of the two weapons)
RMT_Locker - Spawns both weapons at the same time in a weapon locker
The same can be applied to the Flak ammo, in the line AmmoItemSettings[7].