There is a difference between short term RV and long term RV. It is of course not useful to take a short term RV position with a relative value of 5bps if it will have a range of 4-6bps in the foreseeable future, but in the long term it is likely to be positive.
The effects you mention are valid reasons why bonds from the same issuer cannot be fully priced from a singular credit curve. There are others. Take a European government bond curve for example and the reasons why a bond may be cheaper/more expensive than the derived curve might be:
- Nominal and free float in issue, impacting liquidity.
- On the run/ off the run liquidity status.
- Transparency of the price as a CTD of a futures contract.
- Coupon effect (i.e. size of coupon) and corresponding cost per 1eur nominal.
- Monthly series (i.e is it the Mar-Sep coupon series or the Jun-Dec series) for stripping.
- Whether there is a Collective action clause (CAC), i.e. it was issued after a certain date.
- The underlying repo market for the bond and whether the bond can be included as GC in specific tenor buckets.
- Probably more...
As a trader I tried to employ certain techniques to evaluate the 'short term' RV by stripping out the 'long term' RV. I would not be adverse to adjusting the OAS/spreads although this would not necessarily be the only way of doing it.
In a completely generalist way you are building some pricing (curve) model, $T_{\theta; \phi} $, with some (fixed) hyper-parameters, $\phi$ and some variable (calibrated) parameters, $\theta$ that attempts to price your set of bonds with minimal deviation from market prices;
$$ \min_{\theta} \sum_i || T_{\theta, \phi}(b_i) - P(b_i) ||^2_2 $$
where $P(b_i)$ is the price of bond $i$ in your set.
The fact that you might vary some of the fixed hyper parameters, $\phi$, i.e. the interpolation style of the curve, or whether you permit the OAS spread flexibility or/not should not matter, it is simply a model which you can backtest for its generalist predictive power and choose to adopt it or not.
EDIT
The difference between long term RV and short term RV is a matter of holding period of your trade. Suppose you construct a credit curve and value two bonds against it: bond1 (10Y) is 5bps cheap and bond2 (10Y) is 5bps expensive. You might instinctively think it is better to buy bond1. But a historical analysis in the last year suggests bond1 was, on average, 7bps cheap and bond2 was, on average, 7bps expensive to your model. Now if you are to investto hold to maturity (long term) then bond1 is a better purchase on an RV measure. Your standardised mode of valuation has been to equate the cashflows without further considerations, and that is sound from a HTM perspective. If you are taking a trading position for the next 2 months then it may well be that bond2 is a better purchase, since it may well revert to its more expensive mean state in the short term. In this case it would have been better to attempt to strip out the nuances of each bond first before conducting the RV analysis, whatever those nuances maybe (possibly OAS).
There is no unified theory for what you are asking and it requires your own subjectivity and perspective, as well as how it will be incorporated into your risk management.