The BHA has been approached for comment and asked to confirm whether it barred Mr Incredible from running.
Racing's ruling body intervened in recent days, questioning whether Mr Incredible showed sufficient form during a recent race at Kelso, when he started but pulled up, even though connections had been pleased with the horse's performance.
For the past seven weeks the horse therapist Freddy Steele had been working with Mr Incredible.
He told BBC Sport the horse was showing "progress" at home and on the racecourse, and was responding well to the use of "natural horsemanship" techniques.
Mr Incredible's behaviour at Kelso was referred to the BHA by the stewards, who said he was "unruly" and appeared to pull himself up after the 14th fence.
The nine-year-old has won two of his 16 races and finished second four times.
But he has been pulled up in three of his last four contests and refused to race on the other occasion.
Despite his unpredictable behaviour, Mr Incredible was runner-up in the Midlands Grand National last year when based with Irish champion trainer Willie Mullins.
He was considered one of the leading contenders for the 2024 National and was sent off at odds of 10-1 but dwelt at the start and unseated rider Brian Hayes at The Chair.
Mr Incredible had also unseated Hayes in the race 12 months earlier at the 24th fence after his saddle slipped.
"It was 100% the BHA's decision. We appealed it. Their concern was that he would disrupt the start," said Thomson.
"My defence was that he has never disrupted any start. Having got him started at Kelso I saw no reason why he wouldn't start in the Grand National, and having more horses around him would have helped.
"The other thing they said was about his recent form, but their criteria said they would take into account the last six runs and that included second in the Midlands National. It was a totally unsatisfactory situation."
The horse switched stables to join Thomson in December.
Owner Manclark, 85, competed for Great Britain in the luge at the 1968 Winter Olympics in Grenoble, France.
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