Do you know maybe when creating new seed in Electrum if by chance I get all words that are BIP39 compatible (without "special" words unique for Electrum word list) can I recreate that seed on BIP39 wallet?
You will definitely get a seed with bip39 words only because that's been the default behaviour of electrum since version 2.0. However it won't be a bip39 seed and you won't be able to restore it in other bip39 wallets. Wallet software has to support electrum seeds for you to be able to restore in it.