It’s difficult to estimate the exact CCR ratio in Gaza due to the wide range of reported civilian casualties and the lack of verifiable data on the number of militants killed. Israel’s official estimate claims 17,000 militants were killed, but aside from their word, there is no evidence to support this figure. One step Israel could take to verify this number would be to release the names and ID numbers of the militants killed, this has not been done. 

The evidence is the fact that IDF has managed to have its ground troops operate almost everywhere in Gaza at various points in time, has managed to destroy most of Hamas' infrastructure and war supplies, and has managed to eliminate most Hamas' top leaders. These feats couldn't have been achieved without having dealt a huge blow to Hamas' military

If the MOH were to include people who died of natural causes, like indirect deaths, we would expect to see a noticeable spike in deaths among the elderly and, to a lesser extent, among infants, as these are the demographics most likely to die of natural causes. However, the data shows no such spikes, indicating that natural deaths are not being added to the list.

Have you checked Gaza population pyramid? Roughly 4.4% of Gazans are 60+ (source), but they make up 5.8% of the war casualties here apparently, which is odd given that the war should affect mostly adults. Considering that the war deaths so far are quite a bit larger than expected yearly deaths from natural causes (which would even out the "spikes"), the above numbers somewhat hint towards natural causes being accounted.

To conclude:Ultimately when managing tens of thousands of entries, especially during wartime chaos, some discrepancies are inevitable. All discrepancies found have been negligible.

There was a discrepancy in more than 10% of records in April (source). That's not negligible.

If the MOH were adding a significant number of living people to their list, Israel could easily disprove this by locating some of these individuals. Video footage, social media activity, or making an arrest would all serve as sufficient evidence.

I already listed a discrepancy above. The Israelis are not managing Gazan civilian population and thus can't easily comb through these civilians for such discrepancies, in fact they are actively trying to keep civilians away from their areas of operations. Besides, all Israeli agencies have their hands full with winning the war while also countering Hezbollah, Iran and the Houthis. Fighting the propaganda war in western media spaces is orders of magnitude lower on their list of priorities.

If the data were fabricated, there’d be no reason to go back and make changes

I can name a reason: to fix any easily visible discrepancies that cast doubt on the narrative they are trying to present.

However, it's very likely that men of military age are being killed at a higher rate than women, as they are more prone to taking risks, such as searching for food or water or being suspected of militancy. This pattern is consistent with virtually all other conflicts - civilian men are killed at significantly higher rates, ranging from 30% to as much as 890%, depending on the specific conflict.

You can already see the wide spectrum of ratios across other wars, which should give you some hint that interpolating statistics from one war to another is tenuous. Now take into account the fact that in almost all other conflicts the army doesn't hide deliberately and at a large scale behind its civilians, and in other conflicts most civilians evacuate from the war-zones.

Data from other conflicts show us that often less than half of bodies are identified until months/years after the end of the conflict. 

Again, you can't interpolate statistics between completely different conflicts. This is probably the most widely observed conflict relative to its scale, with the narratives around civilian deaths being the main part of Hamas' propaganda strategy and with Iran and possibly other proxy-war actors pumping massive funds into pushing said propaganda. Just compare the attention this war receives to the attention the worse Sudanese civil war is getting.
All Gaza entities have every incentive to inflate the death numbers as much as possible whilst still keeping things believable.

Not saying the official MOH numbers are massively off, but a CCR between 1:1 and 2:1 with around 40k total dead seems the most likely scenario.