Is there a way to save datastore values besides using IntValues?

You don't have to use IntValues. You can store numbers, strings, arrays, and dictionaries in DataStores directly. You can store the coordinates as a dictionary (say, {x = 1, y = 4.5, z = 9} and upload that dictionary into a DataStore.

EDIT: Since you asked, here's how I would do it.

local DataStoreService = game:GetService("DataStoreService")
local modelStore =  DataStoreService:GetDataStore("ModelStore")

-- Encode the part as a table and
-- return a dictionary.
function SerializePart(part)
    local serializedPart = {}
    serializedPart.Position.x = part.Position.x
    serializedPart.Position.y = part.Position.y
    serializedPart.Position.z = part.Position.z

    return serializedPart
end

-- Decode the table generated from SerializePart
-- and create and return a part out of it.
function DeserializePart(serializedPart)
    local part = Instance.new("Part")
    part.CFrame = CFrame.new(
        serializedPart.Position.x, 
        serializedPart.Position.y, 
        serializedPart.Position.z, 
    )

    return part
end

-- Encode each part of the model and
-- return it as an array of serializedParts.
function SerializePartModel(model)
    local serializedModel = {}
    for _, part in pairs(model)
        if part:IsA("Part") then
            local serializedPart = SerializePart(part)
            table.insert(serializedModel, serializedPart)
        end
    end

    return serializedModel
end

-- Decode each part in the array 'serializedModel'
-- and return a model from it.
function DeserializePartModel(serializedModel)
    local model = Instance.new("Model")
    for _, serializedPart in pairs(serializedModel) do
        local part = DeserializePart(serializedPart)
        part.Parent = model
    end

    return model
end

local testModel = game.Workspace.Model
local serializedModel = SerializePartModel(testModel)

modelStore:SetAsync("testModel", serializedModel)

-- later, when we want to retreive testModel
local DataStoreService = game:GetService("DataStoreService")
local modelStore =  DataStoreService:GetDataStore("ModelStore")
local serializedModel = modelStore:GetAsync("testModel")
local testModel = DeserializePartModel(serializedModel)
testModel.Parent = workspace

This will only store the Position of the part, not its Size, CFrame, Color, etc. I have not tested this, but this should work. Maybe.