without using any 3rd party extensions like Metamask, or IDEs like Remix
This suggests a fundamental misunderstanding. I don't think things will make sense until this is resolved.
IDEs like Remix
Avoiding IDE is like saying I want to write a story without using an editor.
Extension like MetaMask
Avoiding user-side wallets is like saying I want to make a web site without bothering with browsers.
Developers have a wide variety of tools they can use at different stages. Let us explore different concerns and how the tools can help.
Early Development Stage
Remix is ideal for fiddling with code. You can write smart contracts, compile them and interact with them at no cost and with near-instantaneous feedback. This helps you confirm your contracts compile and are feature-complete.
You can use the Ethereum testnets to deploy your contracts in a realistic setting. Testnet Ether (to pay for gas) is available free for the asking from Faucets run by volunteers. It's given away for free because it has no economic value. It this setting, you will wait for confirmation and pay for gas so you and your users can see a realistic simulation of how the DApp will work.
Deployment, UI and Unit Testing
One can work out the smart contract with Remix. Truffle is useful for deploying contracts to blockchains (testnet or mainnet), organizing and executing unit tests for the smart contracts and it creates an abrastraction layer and cleaned up syntax for the user interface. That will help make the UI code readable and more understandable from a developer perspective.
It is, of course, possible to interact with the contracts using lower-level calls, possibly down to the level of JSON RPC but that probably wouldn't make the task easier overall. The contract abstraction was created precisely to make the UI coder's life easier.
Tools do indeed introduce learning curves. One has to learn how to use each tool and learn when to use them, but avoiding the use of tools is seldom the answer.
Hope it helps.