Yes. MTD is about how records are kept and returns are submitted, not how VAT is calculated, so every scheme is in scope. What changes is the detail of what you record. Flat rate users keep digital records of supplies made and received but do not need the same level of input tax detail, since you are not reclaiming it in the normal way. Cash accounting users record by payment date rather than invoice date. Retail schemes and the margin scheme have their own record requirements. Any HMRC-recognised software handles the common schemes, but it has to be configured correctly at setup — a flat rate business set up on standard VAT will produce confidently wrong returns for as long as nobody checks.