Does it matter for tax purposes how the price gets split between goodwill and equipment?

Yes, considerably, and this is one of the most heavily negotiated tax details in an asset sale. Goodwill and equipment are taxed very differently: goodwill is generally treated as a capital asset producing a capital gain for the seller, while equipment has usually been depreciated for tax purposes, so its sale can trigger recapture of prior depreciation, taxed as ordinary income rather than as a capital gain, if the sale price exceeds its remaining tax value.

Because of this, sellers often prefer more of the price allocated to goodwill, where the tax treatment tends to be more favourable, while buyers often prefer more allocated to equipment and other depreciable property, since that gives them a higher tax cost base to claim depreciation against in future years. These preferences pull in opposite directions, which is exactly why allocation is negotiated as part of the deal rather than following some standard formula.

The purchase agreement should set out the agreed allocation specifically, asset class by asset class, because both parties are expected to report consistently with it on their own tax filings, and a mismatch between what each side reports is a common trigger for a CRA inquiry.