Random regressions due to lsp overriding user settings via `lsp-register-custom-settings`

Thank you for the bug report

[X] I am using the latest version of lsp-mode related packages.
[X] I checked FAQ and Troubleshooting sections
[X] You may also try reproduce the issue using clean environment using the following command: M-x lsp-start-plain

Bug description

Commit 782e1dc15a590ae9aa2c9b7e39c4cc8a65952e13 by @LaurenceWarne introduced a regression and broke mypy completely for me. That happened, because I had set the same lsp-server settings that the commit modified.

Further research shown that there's nothing wrong with the commit per se, instead the problem is in how lsp-mode handles lsp-server settings. Whatever user sets with lsp-register-custom-settings is being overwritten by lsp-mode, leading to random problems like this one.

Instead lsp-register-custom-settings should not overwrite settings that a user has set.

Steps to reproduce

Create /tmp/.emacs with the following content:

(package-initialize)
(use-package lsp-mode
  :config
  (setq lsp-log-io t)
  (lsp-register-custom-settings '(("pylsp.plugins.pylsp_mypy.enabled" t t))))

Start emacs as emacs -Q -l /tmp/.emacs test.py
Start lsp-mode in the test.py buffer by evaluating M-x lsp
Switch to buffer with communication log by evaluating M-x lsp-workspace-show-log
Search for word pylsp_mypy and look at the value of enabled just below the pylsp_mypy line

Expected behavior

It is true.

Which Language Server did you use?

pylsp

OS

Linux

Error callstack

No response

Anything else?

No response

emacs-lsp / lsp-mode