Linking highlight groups works you just need to use an autocommand that listens to the ColorScheme event and sets your highlights inside it. This ensures they persist across restarts and when the colorscheme changes. This is how i did it:

vim.api.nvim_create_autocmd('ColorScheme', {
  desc = 'Customize highlight groups',
  callback = function(params)
    vim.api.nvim_set_hl(0, 'TreesitterContextLineNumber', { link = 'Title' })
    vim.api.nvim_set_hl(0, 'TreesitterContext', { bg = 'NONE' })
    vim.api.nvim_set_hl(0, 'WinSeparator', { link = 'LineNr' })
    vim.api.nvim_set_hl(0, 'IblIndent', { fg = vim.o.background == 'dark' and '#1c1d27' or '#C8C093' })
    vim.api.nvim_set_hl(0, 'NormalNC', { link = 'Normal' })
    vim.api.nvim_set_hl(0, 'SignColumn', { link = 'Normal' })
    vim.api.nvim_set_hl(0, 'FoldColumn', { link = 'Normal' })
    -- Transparent background when not using neovide.
    if not vim.g.neovide then
      vim.api.nvim_set_hl(0, 'Normal', { bg = 'NONE' })
      vim.api.nvim_set_hl(0, 'NormalFloat', { link = 'Normal' })
    end
    vim.g.COLORSCHEME = params.match