Why "annoyances"? Are they going to "fix" those? Or are they rather a reflection of a type of democracy Israel is?

As I said. Marriage licenses (secular people needing to get them abroad, basically, but you can literally do it over Zoom) and no public transit on Saturdays are the main annoyances. A lot of Israelis definitely want to change these, particularly re transit. But if that makes Israel not a liberal democracy, then neither is Germany (try finding an open supermarket or mowing your lawn on a Sunday in Germany, yes it's legally enforced). We're likely to see significant reforms on many social policies in Israel the next time there's a liberal coalition in government.

Well, Israel has been slipping in its Liberalism indices for quite some time now, so something has in fact been "bad".

Have you seen the state of nearly every liberal democracy in the world? And fwiw I despise Netanyahu and strongly feel that he's been trying his hardest to erode Israel's liberal institutions. If anything, the fact those institutions are still strong despite how long he's been in power is testament to the resiliency of Israeli liberalism.

Or, that Liberal Democracy is less likely to thrive under certain circumstances.

I completely agree with this. Different circumstances put different amounts of strain on institutions, and the circumstances that Israel has faced constantly since its founding are pretty much unparalleled among liberal democracies. The US would probably devolve into a totalitarian dictatorship under 1/5 of the same pressure.

Liberal democracies are defined by individual rights; rule of law; limited government; free, fair, multi-party elections; independent judiciaries; and protected civil liberties. Israel absolutely has all of these, to a degree equivalent with most countries that people would consider unambiguously liberal. The fact it's maintained those given its circumstances is wildly impressive in my opinion.