Much of the work for integrating the tools and machines you buy from outside is highly risky because you dont know the outcome and especially how much the project will cost. It practicalle separates you from the competitors as everyone and his brother can go and buy the latest lithography machine from Nikon.
The equipment? You can have a fairly good idea of how much it costs (acquisition costs, MH) and with that you have a pretty good idea for a starting point for valuation and sale.
The entire point of R&D being OPEX is that you have a cash outflow for a possible 0 benefits. In the case of an equipment, now matter how much you have to tweak it you should have *some* value and it *should* be related to acquisition and MH invested.
I mean the understanding of what is r&d is oldstyle and the tax authorities have no chance to evaluate the reasoning when its unclear even for those working with it.
How you see the balance sheet and income statement isn't how the tax authority does. Somethings deemed as assets the tax law wants as expenses, and vice-versa. Some kind of equipments and facilities have accelerated tax depreciation, some have below-par depreciation rates, etc.
Maybe in the era of the "me too" drugs you are making a fair assessment and the tax law must change, but there are cases where the current law helps. Think about AMD and Bulldozer. AMD spend years with huge negative cash flows, but as most of the R&D was deemed OPEX it also got huge losses in the balance sheet and because of that had to pay 0 corporate income tax in the last few years. When Bulldozer fizzled the impact was 0, because everything was already off balance sheet.
But, what if you deemed Bulldozer R&D an asset? AMD would have experienced a huge cash outflow (because regardless of how you treat the expenditure it still happens), but that would be aggravated by the corporate income tax they would have to pay. And what would happen once Bulldozer fizzled? AMD would have to write off the value of the Bulldozer IP from their portfolio, and only then they would not have to pay income taxes (varies from country to country, in a few they would have to depreciate the asset at normal rates without any tax benefits), and that would make the company's situation far worse.
So in the end, while there are clear cases of abuses of the system like the "me too" drug companies, the system as it is today gives more comfort to companies willing to invest in R&D.