"Say she is treated as dying in estate then everything goes to him. "
Not necessarily. It all depends on the value of her estate.
If you add up the whole value of her estate, including her 50% share of the house and any money in her own name etc then if that comes to less than £322,000 then, yes, everything goes to your dad if they were married at the time of her death.
If her estate is worth more than £322,000 then your dad gets the first £322,000 and then anything over that amount is split 50/50 with any children or grandchildren of your mother.
So, let's say that your mum's estate is worth £422,000 in total. In this case, your dad would get the first £322,000 and then with the remaining £100,000 it would be split with him getting £50,000 and the other £50,000 being split between any children of your mother.
However, if you want your dad to get everything then you can simply pass your share of the money on to him.
"Jointly, their estate is less than £1 million. Does this means that in the event of his death, it will be under the threshold as I think her allowance is taken into account?"
If a person leaves everything to their surviving spouse in a will then, yes, there is no inheritance tax to pay. Your dad will also be able to make use of your mum's allowances as well, which is where the £1 million figure comes from.
However, that £1 million figure is made up of two different things. Everyone has an allowance of £325,000 so 2 x £325k = £650k
There is also an allowance of up to £175,000 each if you leave your main residence to a direct descendant. 2 x £175k = £350k and £650k + £350k = £1 million
The amount you can claim depends on the value of your property. So, for example, let's say your parent's house is worth £300k net after any mortgage. This would mean that your mum's share of the house is worth £150k.
In that case, she (or, rather, the executors) could only claim £150k not £175k
However, if she has died intestate and the estate goes to your dad then I don't think that the allowance for the main residence will pass to him.