I kind of think this might be asking the wrong question.
If you are keeping the bike as a classic, then any mods will reduce its value as a classic. OTOH, by doing mods to the bike, you are depleting the supply of unmodified stock bikes from the market and by that token increasing the value of the ones without mods.
If you are talking about near-term resale value, then you are definitely not increasing the resale value with the mods, not in any measurable way, and you might be reducing it somewhat. You are certainly restricting the market for the bike. Whether we like it or not, the truth is Triumph was way better at marketing and market research than each of us are, so a bone stock Bonneville will have the broadest possible appeal. You might like it better with your mods, but you are reducing the number of people total who will like it at all.
These air-cooled Hinkley twins are in an interesting spot in their history. The oldest of them are not yet old enough to be "classics" or to have any kind of collector value, but they are getting close. The newest are old enough to not compete well on the resale market with their water-cooled cousins. This situation will change soon enough. When the oldest start to be over 20 years old, we'll start to see their value creep up as collectibles, and in that case the stock ones are going to be in highest demand. That's just a couple of years away.
This whole situation reminds me of when I had a '72 Datsun 240Z, back in 1993 thru about 1997. Really wish I still had that car! But I had the car during the same kind of dark time in its history. My mostly stock, mostly rust-free car in the mid 90s was worth $1500 or so. Ten years later that same car was worth 10x that. My Z in the condition I let it go today would be worth at least $30K. In fact, I have the original red seats with on tears in them still in my garage, and given the rarity of the red interior, I think those stock seats may be worth more today than the whole car was worth in 1997.
So the day may be coming when the stock exhaust, handlebars and seat from your Bonneville will be worth more than the whole bike with modifications is worth today. Imagine how hard it will be to find a stock set of rear shocks for a Bonneville SE in 20 years. Or a stock set of headlight ears. Or a stock rear fender, especially with the taillight/turn-signals/license-plate in original chrome. Only show bikes will have those parts on them and we'll all ooh and ahh over them even though today we toss those parts in the bin without a second thought.