Hi JB,
It will make a considerable difference, knowing what the variety of waterlily is like.
If anything, some waterlilies might better be planted so they are restrained, large aggressive growing varieties with poor leaf to bloom ratios are likely to romp all over the place with just a rock placed on them, the roots produced in self protecting masses so harsh root grazing hardly matters.

Wherever an odorata hybrid might be planted, its quickly going someplace else

A caveat, some waterlilies are robust enough to cope with planting any old whooo, others, are not.

Others need a bit of coddling and will not respond at all well to root grazing especially the Marliacs which like their roots to be very well established before they go into prolific blooming cycle

The current water quality may be a factor, if the pond is filtered heavily and low in minerals, making the pot and its soil accessible for regular nudges of fertiliser would be a priority, choosing a potting media which helps to retain fertilisers

If the pond is normally very fertile with heavy algae blooms, heavy handed fertilising might be very regrettable

If your pond is subject to very volatile swings in temperature, time release fertilisers may go from doing nothing when the roots need to develop in the cool months, to scorching delicate root tips when the more soluble corrosive chemicals are released following rapid temperature swings

A big volume pond that has very stable temperature fluctuations is where lilies can give off their best, a 'hot' mix, similar to Perry's recipes might push a coarse variety into a nasty riot of foliage and growth, while a sedate Marliac would be perfect sight... The coarse variety might better have been planted with a very very lean mix and turned out to be a far more pleasant option

Reference for Perry's 'showpiece' recipe:

A lot of fellow water gardeners have asked
what I do to get large lily pads with five to seven
blooms on each plant. I tribute this to an article I read
by Perry D. Slocum in the March 1997 edition of the
Water Garden Magazine. Perry’s article briefly
covered different recipes they had used over the
years on their display gardens. He gave a detailed
recipe of “How to grow the biggest blooms” after
many years of experimentation.
Perry’s tub measured 23” across x 12” deep.
The tubs I use are 17” across x 8” deep so the
quantity of materials was slightly altered. I also used
Fertiloam 9-13-7 New Law Fertilizer instead of the
Miracle Grow 10-20-15 from Perry’s recipe.
Starting at the bottom of the tub, I use the following
steps:
1. 1” of mostly clay soil finely tilled. A little sand is
okay.
2. 1” of composted (bagged) cow manure mixed
with the soil from step 1.
3. 2/3 cup of bone meal spread around the outside
perimeter of the tub, on top of the manure and
soil mix.
4. Using a 3 lb. coffee can, mix one can of tilled
clay soil and one can of composted cow manure
in a separate container. Spread the mixture on
top of steps 1-2-3 in the tub without disturbing
the bone meal placement.
5. 3 Tablespoons of Fertiloam New Lawn Fertilizer
9-13-7 spread evenly over the top of steps 1-2-3-
4.
6. 5 Pondtabs 10-14-8 (planttabs Aquatic plant
food). Use a wooden dowel or small broomstick
to push the tabs to the bottom, spaced evenly
around the outer perimeter of the tub. Pack the
hole tightly with clay.
7. 1” of finely tilled clay on top of steps 1-2-3-4-5-6.
8. One Hardy Lily rhizome of your choice. Make
sure you wash off any soil from the previous pot,
coat any cuts or division with an anti-fungal
powder. Trim off excess roots. Plant the rhizome
in the container and firm down soil and rhizome
firmly.
9. 1” of pea gravel pressed firmly over the mix and
rhizome. Place a stone or half brick over the
rhizome or it will float out. Water heavily with
pond water before placing your plant in the
water. Firm it again. This will help to keep it from
floating out of the unsettled mix

Reference for Marliac varieties:
Cultivation notes, direct from the horses mouth, so to speak:

'A depth of 2 feet is enough for the tanks. A bed of earth 6 inches deep on the bottom of lie basins will be sufficient for the culture of Water Lilies. It ought to be as free as possible from gravel and stones. The best kind of earth is heavyish loam from the garden or meadow, but earth composed of leaf-mould and alluvial soil is also very suitable. One can also make a mixture of them, but it is better not to put with them any fresh manure which is still undergoing fermentation.'
-Marliac

(Bear in mind Marliac was not a fishy keeper, he may not have given a hoot about the priority of topping the loam with stones, needless to say, in those days fertilisers were largely the exclusive monopoly of four legged manufacturers rather than industrial conglomerates)

Regards, andy
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