In the future, I would suggest the other direction. Ask me or Stefan to close the ticket at the Eglot tracker.
Anyway, I think this two-liner patch fixes the problem and doesn't have any unintended side-effects for M-x eglot-reconnect.
diff --git a/eglot.el b/eglot.el
index ff94d5ca5f..3b1b1a9536 100644
--- a/eglot.el
+++ b/eglot.el
@@ -796,6 +796,8 @@ treated as in `eglot-dbind'."
:documentation
"Represents a server. Wraps a process for LSP communication.")
+(cl-defmethod initialize-instance :before ((_server eglot-lsp-server) &optional args)
+ (cl-remf args :initializationOptions))
;;; Process management
(defvar eglot--servers-by-project (make-hash-table :test #'equal)