If disagreement is a natural thing among people, how then does the Bitcoin community make changes to the Bitcoin network?
It is simple: you have the current version, which is up and running. If there is enough support to make an upgrade, then people can do so. But most of the time, the "status quo" is preserved, and nothing is changed.
Also note, that there are many things, which can be done, without touching consensus. For example: if you want to compress transaction data, you can do so without any forks. And there are many kinds of BIPs, including a lot of those, which are "Informational", which means, that they are fully optional, and you can implement them, or skip them, if you want.
Though, I find it difficult to identify which BIP has been approved and which one haven't.
You have a large table in the README file:
https://github.com/bitcoin/bips/blob/master/README.mediawiki (it is visible in the front page, but you probably didn't scroll enough to see it). You have a column called "Status".
But this entire process requires the approval from about 95% of the miners, that agrees to it when mining a block.
It depends. Historically, different BIPs had different activation rules.
1.Could anyone help me identify between the BIP that have been approved by the community and those that are just proposed.
See the "Status" column, mentioned above.
Can't the new upgrades be implemented even with such percentages?.
There are many different kinds of changes:
1. Hard-forks: highly discouraged, the nearest one can happen in 2038 or 2106, people try to avoid it at all costs, because then you can easily create an altcoin, instead of improving Bitcoin.
2. Soft-forks: this is something like Segwit or Taproot, but we had some smaller soft-forks, which are less known, but also important (for example BIP-42).
3. No-forks: those changes are done on a regular basis. For example: HD wallets, compressing transactions, signing messages, UI changes.
Also note, that there are some second layers, where you can experiment with features, without deploying it on mainnet, for example millisatoshis in LN have no on-chain representation.
does the decision of the 95% override those who are against?.
It depends on activation rules, but yes, if something is activated, then to deactivate it, you need another soft-fork (because "just turning it off" could lead to a loss of funds).
are there other perfect times these implementations can be done ?.
Well, sometimes things are scheduled, and sometimes not. For example, fixing Value Overflow Incident was never planned in advance: it just happened, and required an immediate reaction. The same with fixing total supply: there was just some simple commit, and the whole BIP was created later, to explain, what happened, and why it happened.