The garden mechanic is a bit wonky in the initial game as follows:
You don't enable the garden until your aunt comes around again. This gate doesn't make sense at all. MC is from the boondocks and doesn't know what a garden looks like the first time they check around the house? Odds are extreme they were following ma and pa around in the home patch as soon as they learned how to walk. They are cooking for themselves so obviously know how to cultivate all the usual suspects for salads, veggies and herbs to go along with the meat main course. That garden would have been discovered and put to use probably on the first day. There would be some obvious need for weeding, but rocks? That stuff doesn't move or get dropped by birds that fancy themselves as bombers. Those would have been removed by the aunt or the granddad when the shop first got established. OTOH there might be some fast growing, bird planted trees that need removal.
I think the garden arc should go as follows:
Garden is enabled the first day as soon as MC does the walkaround and thus finds it. He spends a day weeding and getting the compost pile set up again with the proceeds. Now the "check the garden for seeds" entry in your inventory will actually make sense rather than being some odd appendage on that page in the early game. The seeds in stock for the garden would be the usual suspects, but they may or may not be viable. The garden itself should have some basic perennials and self-seeding annuals that MC should recognize as herbs for cooking and pickling, good flowers for the pollinators, or deer and bug repellents. That would include the fennel and chamomile, sage, oregano, thyme, dill, chives, garlic, lemon balm, bee balm, rosemary, vines like blueberry, raspberry, blackberry and goji berry and pokeweed. I would argue that MC already knows about the chamomile being a relaxing tea as well as a pollinator flower. They use the fennel in pickling but may not know whatever mechanic it has in an apothecary. They probably know the pokeweed is a good way to keep birds around for bug removal so not really a weed. So auntie's return is now merely a way to find out about the apothecary uses for stuff MC already knows about.
--edit--
By the way, it's counterproductive to "churn up the soil" aka tilling. If any of my ranting is making sense for you IRL then you may want to look at the
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youtube channel. Here's how and why you do
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