My response in your original issue was overly terse, I apologise for that.

There's several suggestions/issues here that I can see.

• Show advanced signals button
  I'm confused about what you want. The button was added in response to comments (mostly from yourself) about how the setting to reenable signals was hard to find. But now you don't want a way to enable them? A pop up window isn't viable - we can't possibly add such a mechanism just for signals, nor do we have any feasible way of detecting when the game has been upgraded
  (Improving the settings window is a separate, ongoing, discussion)

• Convert signals button
  Might be some legitimate issues here. I agree that its use is limited - I don't think I've ever used it

• Hide semaphores
  This has come up several times, we've never been able to come up with a good way of switching between the two. Perhaps the convert signal button could be converted to toggle between the two types, and overbuilding would "just work" (tm)? That might work.

• Change default signal separation
  Why? You haven't provided any justification here

• Signal window looks strange with BRIX
  This is the actual size of the sprites. They appear to have a lot of blank space (I'd consider it an issue of the NewGRF) - there's no way to detect the transparency without a lot of effort (it would be slow).

• Place one-sided block/pre-signals first
  This seems like a good suggestion to me

And as ever:

We cannot add settings for every usecase. We have too many already and are actively working on reducing them. Sorry about that.

Show advanced signals button
I don't think this is helpful for new players. Asking them questions in a field they don't know yet won't make anything easier for them. And when it comes to showing tips, a great many, even much simpler games, have a tutorial mode. Meanwhile, here in much more complex OTTD isn't and it would be very advisable to create a game mode where the player could learn step by step all, or at least the most important elements of the game, such as "Building roads / tracks"> "Putting basic signaling"> "Creating basic orders" > "Vehicle duplication"> "Advanced signaling"> etc. There, when performing tasks, such larger messages could appear, even with graphics. But... well, realistically, it's more of a fantasy zone, but the Help and manuals window project #7786 is open and that could also be of great help to new players.
Another idea might be to add (exclusive) question mark icons where the player might have some problems or doubts - even anywhere. I showed something in this direction on one of the versions of the improved finance window - here

Convert signals button
As it stands, it's one of the most useless features in the game for me. It doesn't matter much to me, but I agree with Rau here that this button would be much more useful if the signal shift was area-wise and not one-piece. Then it would be useful to be able to disable the selection of a specific signaling device (or by default any wouldn't be selected), thanks to which it would be possible to simultaneously convert different types of semaphores to signaling devices and vice versa.

Hide the semaphores
You don't like it, but for me the best way would be to add an option to disable semaphores entirely. Many players don't want to use them at all. Alternatively! What would be simpler, if somewhat hidden, might also be that setting the signals appearance date to year 0 will disable the semaphores (also using Ctrl while building will not build the semaphore). Sample explanation for setting: "Choose 0 to disable semaphores completely."

First, place a one-sided block/pre-signal
Yes, I think it could be better than it is now. Using the bidirectional variant usually only ends in problems and you have to know how to use it, so it's not good that it's the default. I also think that this behavior should apply to all signals. Certainly a bidirectional entry signal doesn't make sense as a basic option. Then only two out of five remain, where the use of unidirectional is similarly frequent or even more frequent than the use of bidirectional. From my point of view, this is not a big change. While it is about player habits, it seems beneficial enough that it will be fairly easy for players to get used to, so I don't think it's necessary to add options.

"We have too many already (settings) and are actively working to reducing them."
I understand the reason, but... heh... I think that's the wrong approach. Perhaps there has been more of this recently, but I've known two instances of deleting a setting, and both are really frustrating.

The first case is to remove the option of no planes crashes. First, it destroyed a lot of my save files, forcing me to use the cheat option, which I really don't like and don't think I'm alone in that. Second, I am currently working on updating two scenarios for two popular online servers and this change has prevented me from using the best setting whereby the profits from transporting passengers by air would be reasonably limited while transporting other goods could still generate some profit. With this option removed, there is no way to reasonably balance it - there is always some shit. It's really discouraging.

The second case was the last deletion of the default signaling type setting. Generally, it doesn't matter to me, because I use all of them anyway and often start with something other than the default one. However, the frustrating thing is that now each time I run a different version of the game, the signaling settings are different - the ones that limit the availability of signaling types are constantly changing. I have to go into these settings and tweak them every time. I was a supporter of simplifying the signaling for beginners, but the way to make this change is really terrible.

In the past, other settings were probably also removed, which unfortunately means that many scenarios and saves are unplayable today.