You can also go into Items and reduce the healing effect of various items (more easily than reducing the drop rate if you're doing it manually) as well as Skills for healing effects of skills. The lower starting level won't have much impact, levels have lowish impact on stats because of the XP Drain mechanic being sexy not just immediately crippling.
I am trying to make more enemies chase the player (and chase fast enough that they can catch you), which has been promising for increasing the danger level of each stage, but it requires a script since each monster is a unique entity in the Maps files. I've also started creating some new items to replace the current ones and modify some encounters to have extra gimmicks. Those are slightly more involved changes than just making some tweaks here and there.
Another approach to your idea of increasing the number of encounters is to incentivize the player to seek out and actively fight more enemies.
On the previous game I tried to force this by making money harder to gain and having the store be the only source of uncorrupted items. This had the opposite affect and drove players to shy away from fights.
Maybe a rework of some bastes (or addition of new bastes) that require items to be dropped from specific mob(s) or for the player to do specific actions that can only be done mid-fight for removal of that baste. These bastes could be gained on the map due to specific event(s) or triggers to prevent the chance of the player always regaining that baste and them giving up on trying to cleanse it.
Or shop specific equipment (or skills/spells) that are expensive but have great stats/benefits to the player to justify the extra fighting to grind out money. Maybe the gear is equivalent to offsetting the stat loss of 1-2 active bastes but doesn't affect the evasion calculation based on quantity of active bastes (assuming they kept that consistent to the last game).
Definitely the main problem with the game is that most fights can easily be skipped or avoided. There are few reasons to actively chase for fights yourself.
In addition, fights that catches you from behind are the only challanging ones witch will progress your corruption stats (unless you have already been corrupted with bastes). However it is easy to avoid such suprise fights.
Since the enemies doesn't really become stronger statwise in further levels, there is no incentive to go for extra fights. You don't really need to, and the bountiful of chests and random drops covers your need for gear and consumables. Level ups are as you say, minor changes in your stats.
Further than editing the config file, I have no skills in modifying the game to the level you speak of. I do however have some ideas for making fights more meaningful.
Option 1 - when beating the boss of an area, it will inflict you with some Stat decreasing baste. To cure it, you would need some expensive item from the base, or dropped loot.
Would it maybe make sense if going for the loot option to make the loot drop in the next area? That way you have to take some fights with reduced stats.
Option 2 - make level ups more impactful, (more stat increase on level) lower the starting level and make enemies in each zone progressively more difficult. This way you would need to fight for XP instead of dodging fights. Would definitely need to adjust the XP drain baste, and maybe make progress a bit strange.
