Then how can I use the custom "own" finder?

I think you've found a gap in the docs; or at least, the reference to custom finders is perhaps not obvious enough... I have an example of how to do this in my dotfiles:

local has_commandt, commandt = pcall(require, 'wincent.commandt')
if has_commandt then
 commandt.setup({
 -- Demo: showing how to set up arbitrary command scanner that runs
 -- `ack -f --print0`. See accompanying `:CommandTAck` definition below.
 finders = {
 ack = {
 command = function(directory)
 pushd(directory)
 local command = 'ack -f --print0'
 local drop = 0
 return command, drop
 end,
 max_files = 100000,
 on_close = popd,
 on_directory = get_directory,
 open = on_open,
 },
 },
 })
 vim.api.nvim_create_user_command('CommandTAck', function(command)
 require('wincent.commandt').finder('ack', command.args)
 end, {
 complete = 'dir',
 nargs = '?',
 })
end

Finally, is there away to just use the built-in find and fts commands and ignore a set of directories?

Not at this time. I haven't wanted to roll out a bunch of configuration options hot on the heels of the rewrite, but rather wanted to gather feedback and experience with the kind of modifications that people want to make. For now, the horrible-and-ghastly way to override a built-in finder is to look at how they are implemented and effectively fork them by copy-pasting them into your setup() call, giving them a unique name, and customizing them like in the example above.

Having said that, the Ripgrep scanner may come very close to doing what you want out of the box. It will already ignore .git directories, and I believe it will respect a configuration file (eg. $HOME/.ripgreprc if you export the appropriate RIPGREP_CONFIG_PATH environment variable). So you may be able to get it to do what you want without touching Command-T's config at all.