The reference files have the planet bonuses in text format so you can see the elements. This is the PlanetBonusCrystalMiners.entity (from entrenchment/trinity -not sure if rebellion has others)
TXT
entityType "PlanetBonus"
minUpgradeLevelNeeded 1
maxUpgradeLevelNeeded 1
nameStringID "IDS_PLANETBONUS_CRYSTALMINERS_NAME"
descStringID "IDS_PLANETBONUS_CRYSTALMINERS_DESC"
floatBonus:AdditiveCultureSpreadPerc 0.000000
floatBonus:AdditivePopulation 0.000000
floatBonus:AdditivePlanetHealth 0.000000
floatBonus:AdditiveSlotsCivilian 0.000000
floatBonus:AdditiveSlotsTactical 0.000000
floatBonus:AdditiveTaxIncome 0.000000
floatBonus:AdditiveTradeIncomePerc 0.000000
floatBonus:MetalIncomePerc 0.000000
floatBonus:CrystalIncomePerc 0.500000
floatBonus:GravityWellRadiusPerc 0.000000
floatBonus:ModuleBuildCostPerc 0.000000
floatBonus:ModuleBuildRatePerc 0.000000
floatBonus:PlanetUpgradeBuildCostPerc 0.000000
floatBonus:PlanetUpgradeBuildRatePerc 0.000000
floatBonus:PopulationGrowthPerc 0.000000
intBonus:ModuleConstructors 0
intBonus:SpacePonies 0
hudIcon "HUDICON_PLANETBONUS_CRYSTALMINERS"
smallHudIcon "HUDICON_PLANETBONUS_CRYSTALMINERS"
infoCardIcon "HUDICON_PLANETBONUS_CRYSTALMINERS"
You can change just about anything and with some creative writing have something nice or severe. The 'bonuses' can be negative too.
You could make your own mod with your own bonuses/penalties, but you then need to put them in the Entity.manifest and put them into the planet entity files.